In [1]:

    

#libraries
library(GO.db)
library(topGO)
library(org.Sc.sgd.db)
library(GOSemSim)
library(gridExtra)
library(GOSim)


    

    




Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: graph
Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: ‘topGO’

The following object is masked from ‘package:IRanges’:

    members


GOSemSim v2.0.4  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978

Attaching package: ‘gridExtra’

The following object is masked from ‘package:Biobase’:

    combine

The following object is masked from ‘package:BiocGenerics’:

    combine

Loading required package: annotate
Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:graph’:

    addNode

In [2]:

    

file <- "yeast_uetz"

ont <- "BP"
p <- 0.1

db <- org.Sc.sgd.db
mapping <- "org.Sc.sgd.db"
ID <- "ENSEMBL"

##load all community gene lists
setwd(sprintf("/home/david/Documents/ghsom/%s_hierarchy_communities_%s", file, p))

scGO <- godata(OrgDb = mapping, keytype = ID, ont = ont)

setOntology(ont, loadIC=TRUE)
setEvidenceLevel(evidences="all", organism=org.Sc.sgdORGANISM, gomap=org.Sc.sgdGO)


    

    




[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."






    




initializing GOSim package ...
-> retrieving GO information for all available genes for organism 'human' in GO database
-> filtering GO terms according to evidence levels 'all'
-> loading files with information content for corresponding GO category (human)
finished.
-> loading files with information content for corresponding GO category (human)
-> retrieving GO information for all available genes for organism 'Saccharomyces cerevisiae' in GO database
-> filtering GO terms according to evidence levels 'all'

In [3]:

    

generateMap <- function(filename){
    map <- as.matrix(read.csv(filename, sep=",", header = F))
    communities <- map[,1]
    map <- map[,2:ncol(map)]
    rownames(map) <- communities
    colnames(map) <- communities
    return (map)
}

#background gene list
backgroundFilename <- "all_genes.txt"
allGenes <- scan(backgroundFilename, character())

#shortest path files
shortestPathFiles  <- list.files(pattern="*shortest_path*")

#shortest paths list
shortestPaths <- lapply(shortestPathFiles, generateMap)
names(shortestPaths) <- sapply(names(shortestPaths), function(name) strsplit(name, "_")[[1]][[1]])

#communitiy assignemtns
assignments <- as.matrix(read.csv("assignment_matrix.csv", sep=",", header=F))
rownames(assignments) <- allGenes
colnames <- sapply(1:ncol(assignments), function(i) as.character(i-1))
colnames(assignments) <- colnames
    
allGenesInDB <- keys(db)


    

In [9]:

    

shortestPaths


    

    





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In [10]:

    

getDepth <- function(com) {
    return(which(apply(assignments, 2, function(i) any(i == com))))
}

getGenes <- function(com){
    return(names(which(assignments[,getDepth(com)] == com)))
}

getSubCommunities <- function(com){
    return(try(as.character(unique(assignments[getGenes(com), getDepth(com) + 1]))))
}

getSuperCommunity <- function(com){
    return(try(as.character(unique(assignments[getGenes(com), getDepth(com) - 1]))))
}

getShortestPath <- function(com){
    return (try(shortestPaths[[com]]))
}
                       
getNeighbours <- function(com){
    
    superCommunity <- getSuperCommunity(com)
    map <- getShortestPath(superCommunity)
    v <- map[com,] == 1
    return (names(v[v]))
    
}


    

In [11]:

    

communitySimilarity <- function(community) {
    geneSims <- mgeneSim(genes = getGenes(as.character(community)), 
                         semData = scGO, measure = "Wang", combine = "BMA", verbose=F)
    if (length(geneSims) > 1) {
        return(mean(geneSims[upper.tri(geneSims)]))
    } else {
        return (NaN)
    }
}


    

In [12]:

    

layerSimilarity <- function(layer) {
    communitiesSimilarity <- sapply(unique(assignments[,layer][assignments[,layer] != -1]), communitySimilarity)
    communitiesSimilarity <- communitiesSimilarity[!is.na(communitiesSimilarity)]
    return(mean(communitiesSimilarity))
}


    

In [ ]:

    

layerMeanSimilarities <- sapply(colnames, layerSimilarity)


    

In [ ]:

    

layerMeanSimilarities


    

In [10]:

    

plot(colnames, layerMeanSimilarities, xlab="Layer", ylab="Mean Similarity", type = "l")


    

In [14]:

    

enrichmentResults <- sapply(1:max(assignments), function(i) {

    genesOfInterest <- getGenes(i)
    genesOfInterest <- genesOfInterest[genesOfInterest %in% allGenesInDB]
    GOenrichment(genesOfInterest, allGenesInDB, cutoff=0.05, method="weight01")
})


    

    




Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 1848 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 16:	3 nodes to be scored	(0 eliminated genes)

	 Level 15:	12 nodes to be scored	(0 eliminated genes)

	 Level 14:	33 nodes to be scored	(13 eliminated genes)

	 Level 13:	63 nodes to be scored	(116 eliminated genes)

	 Level 12:	93 nodes to be scored	(406 eliminated genes)

	 Level 11:	131 nodes to be scored	(804 eliminated genes)

	 Level 10:	190 nodes to be scored	(1400 eliminated genes)

	 Level 9:	232 nodes to be scored	(2023 eliminated genes)

	 Level 8:	234 nodes to be scored	(2704 eliminated genes)

	 Level 7:	245 nodes to be scored	(3775 eliminated genes)

	 Level 6:	254 nodes to be scored	(4476 eliminated genes)

	 Level 5:	195 nodes to be scored	(4884 eliminated genes)

	 Level 4:	110 nodes to be scored	(5233 eliminated genes)

	 Level 3:	39 nodes to be scored	(5412 eliminated genes)

	 Level 2:	13 nodes to be scored	(5489 eliminated genes)

	 Level 1:	1 nodes to be scored	(5602 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 87 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	2 nodes to be scored	(0 eliminated genes)

	 Level 10:	4 nodes to be scored	(119 eliminated genes)

	 Level 9:	6 nodes to be scored	(132 eliminated genes)

	 Level 8:	7 nodes to be scored	(158 eliminated genes)

	 Level 7:	9 nodes to be scored	(288 eliminated genes)

	 Level 6:	12 nodes to be scored	(808 eliminated genes)

	 Level 5:	16 nodes to be scored	(1897 eliminated genes)

	 Level 4:	16 nodes to be scored	(2368 eliminated genes)

	 Level 3:	8 nodes to be scored	(3947 eliminated genes)

	 Level 2:	5 nodes to be scored	(4428 eliminated genes)

	 Level 1:	1 nodes to be scored	(5113 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 160 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	3 nodes to be scored	(0 eliminated genes)

	 Level 10:	3 nodes to be scored	(11 eliminated genes)

	 Level 9:	7 nodes to be scored	(31 eliminated genes)

	 Level 8:	8 nodes to be scored	(127 eliminated genes)

	 Level 7:	11 nodes to be scored	(240 eliminated genes)

	 Level 6:	22 nodes to be scored	(504 eliminated genes)

	 Level 5:	30 nodes to be scored	(918 eliminated genes)

	 Level 4:	40 nodes to be scored	(2931 eliminated genes)

	 Level 3:	23 nodes to be scored	(4783 eliminated genes)

	 Level 2:	11 nodes to be scored	(5283 eliminated genes)

	 Level 1:	1 nodes to be scored	(5540 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 189 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	3 nodes to be scored	(0 eliminated genes)

	 Level 12:	8 nodes to be scored	(45 eliminated genes)

	 Level 11:	7 nodes to be scored	(279 eliminated genes)

	 Level 10:	7 nodes to be scored	(545 eliminated genes)

	 Level 9:	8 nodes to be scored	(842 eliminated genes)

	 Level 8:	12 nodes to be scored	(1274 eliminated genes)

	 Level 7:	19 nodes to be scored	(1464 eliminated genes)

	 Level 6:	29 nodes to be scored	(2246 eliminated genes)

	 Level 5:	38 nodes to be scored	(2743 eliminated genes)

	 Level 4:	28 nodes to be scored	(3476 eliminated genes)

	 Level 3:	18 nodes to be scored	(4204 eliminated genes)

	 Level 2:	10 nodes to be scored	(4832 eliminated genes)

	 Level 1:	1 nodes to be scored	(5216 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 175 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	3 nodes to be scored	(33 eliminated genes)

	 Level 10:	7 nodes to be scored	(46 eliminated genes)

	 Level 9:	15 nodes to be scored	(121 eliminated genes)

	 Level 8:	15 nodes to be scored	(238 eliminated genes)

	 Level 7:	17 nodes to be scored	(457 eliminated genes)

	 Level 6:	24 nodes to be scored	(887 eliminated genes)

	 Level 5:	33 nodes to be scored	(1544 eliminated genes)

	 Level 4:	32 nodes to be scored	(2457 eliminated genes)

	 Level 3:	17 nodes to be scored	(4205 eliminated genes)

	 Level 2:	8 nodes to be scored	(5246 eliminated genes)

	 Level 1:	1 nodes to be scored	(5526 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 149 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	3 nodes to be scored	(0 eliminated genes)

	 Level 11:	5 nodes to be scored	(0 eliminated genes)

	 Level 10:	6 nodes to be scored	(450 eliminated genes)

	 Level 9:	7 nodes to be scored	(815 eliminated genes)

	 Level 8:	9 nodes to be scored	(913 eliminated genes)

	 Level 7:	7 nodes to be scored	(1022 eliminated genes)

	 Level 6:	25 nodes to be scored	(1365 eliminated genes)

	 Level 5:	37 nodes to be scored	(2337 eliminated genes)

	 Level 4:	25 nodes to be scored	(3388 eliminated genes)

	 Level 3:	16 nodes to be scored	(4390 eliminated genes)

	 Level 2:	8 nodes to be scored	(5294 eliminated genes)

	 Level 1:	1 nodes to be scored	(5540 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 194 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	4 nodes to be scored	(0 eliminated genes)

	 Level 10:	8 nodes to be scored	(2 eliminated genes)

	 Level 9:	11 nodes to be scored	(5 eliminated genes)

	 Level 8:	18 nodes to be scored	(47 eliminated genes)

	 Level 7:	23 nodes to be scored	(186 eliminated genes)

	 Level 6:	34 nodes to be scored	(599 eliminated genes)

	 Level 5:	38 nodes to be scored	(1627 eliminated genes)

	 Level 4:	29 nodes to be scored	(3787 eliminated genes)

	 Level 3:	17 nodes to be scored	(4832 eliminated genes)

	 Level 2:	9 nodes to be scored	(5262 eliminated genes)

	 Level 1:	1 nodes to be scored	(5563 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 372 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	4 nodes to be scored	(0 eliminated genes)

	 Level 13:	7 nodes to be scored	(28 eliminated genes)

	 Level 12:	10 nodes to be scored	(176 eliminated genes)

	 Level 11:	17 nodes to be scored	(451 eliminated genes)

	 Level 10:	24 nodes to be scored	(645 eliminated genes)

	 Level 9:	35 nodes to be scored	(936 eliminated genes)

	 Level 8:	41 nodes to be scored	(1187 eliminated genes)

	 Level 7:	45 nodes to be scored	(1584 eliminated genes)

	 Level 6:	62 nodes to be scored	(2823 eliminated genes)

	 Level 5:	63 nodes to be scored	(3659 eliminated genes)

	 Level 4:	36 nodes to be scored	(4187 eliminated genes)

	 Level 3:	19 nodes to be scored	(4993 eliminated genes)

	 Level 2:	7 nodes to be scored	(5362 eliminated genes)

	 Level 1:	1 nodes to be scored	(5563 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 324 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 16:	1 nodes to be scored	(0 eliminated genes)

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	3 nodes to be scored	(4 eliminated genes)

	 Level 13:	6 nodes to be scored	(4 eliminated genes)

	 Level 12:	10 nodes to be scored	(14 eliminated genes)

	 Level 11:	12 nodes to be scored	(371 eliminated genes)

	 Level 10:	17 nodes to be scored	(748 eliminated genes)

	 Level 9:	29 nodes to be scored	(1068 eliminated genes)

	 Level 8:	31 nodes to be scored	(1361 eliminated genes)

	 Level 7:	34 nodes to be scored	(1704 eliminated genes)

	 Level 6:	51 nodes to be scored	(2661 eliminated genes)

	 Level 5:	57 nodes to be scored	(3205 eliminated genes)

	 Level 4:	41 nodes to be scored	(3840 eliminated genes)

	 Level 3:	20 nodes to be scored	(4876 eliminated genes)

	 Level 2:	10 nodes to be scored	(5298 eliminated genes)

	 Level 1:	1 nodes to be scored	(5569 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 466 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	7 nodes to be scored	(26 eliminated genes)

	 Level 12:	14 nodes to be scored	(40 eliminated genes)

	 Level 11:	24 nodes to be scored	(161 eliminated genes)

	 Level 10:	44 nodes to be scored	(574 eliminated genes)

	 Level 9:	48 nodes to be scored	(1068 eliminated genes)

	 Level 8:	45 nodes to be scored	(1382 eliminated genes)

	 Level 7:	53 nodes to be scored	(1885 eliminated genes)

	 Level 6:	70 nodes to be scored	(2429 eliminated genes)

	 Level 5:	74 nodes to be scored	(3443 eliminated genes)

	 Level 4:	53 nodes to be scored	(4319 eliminated genes)

	 Level 3:	22 nodes to be scored	(4715 eliminated genes)

	 Level 2:	9 nodes to be scored	(5069 eliminated genes)

	 Level 1:	1 nodes to be scored	(5282 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 147 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	2 nodes to be scored	(0 eliminated genes)

	 Level 10:	5 nodes to be scored	(6 eliminated genes)

	 Level 9:	8 nodes to be scored	(75 eliminated genes)

	 Level 8:	11 nodes to be scored	(141 eliminated genes)

	 Level 7:	14 nodes to be scored	(384 eliminated genes)

	 Level 6:	24 nodes to be scored	(870 eliminated genes)

	 Level 5:	31 nodes to be scored	(1994 eliminated genes)

	 Level 4:	28 nodes to be scored	(3783 eliminated genes)

	 Level 3:	15 nodes to be scored	(4628 eliminated genes)

	 Level 2:	7 nodes to be scored	(5355 eliminated genes)

	 Level 1:	1 nodes to be scored	(5553 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 308 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	2 nodes to be scored	(0 eliminated genes)

	 Level 13:	5 nodes to be scored	(7 eliminated genes)

	 Level 12:	7 nodes to be scored	(50 eliminated genes)

	 Level 11:	9 nodes to be scored	(339 eliminated genes)

	 Level 10:	10 nodes to be scored	(574 eliminated genes)

	 Level 9:	14 nodes to be scored	(821 eliminated genes)

	 Level 8:	20 nodes to be scored	(915 eliminated genes)

	 Level 7:	38 nodes to be scored	(1323 eliminated genes)

	 Level 6:	53 nodes to be scored	(2480 eliminated genes)

	 Level 5:	62 nodes to be scored	(3114 eliminated genes)

	 Level 4:	48 nodes to be scored	(3939 eliminated genes)

	 Level 3:	26 nodes to be scored	(4603 eliminated genes)

	 Level 2:	12 nodes to be scored	(4945 eliminated genes)

	 Level 1:	1 nodes to be scored	(5271 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 172 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	4 nodes to be scored	(0 eliminated genes)

	 Level 12:	7 nodes to be scored	(15 eliminated genes)

	 Level 11:	9 nodes to be scored	(280 eliminated genes)

	 Level 10:	8 nodes to be scored	(500 eliminated genes)

	 Level 9:	9 nodes to be scored	(805 eliminated genes)

	 Level 8:	13 nodes to be scored	(913 eliminated genes)

	 Level 7:	19 nodes to be scored	(1474 eliminated genes)

	 Level 6:	28 nodes to be scored	(2186 eliminated genes)

	 Level 5:	35 nodes to be scored	(2401 eliminated genes)

	 Level 4:	22 nodes to be scored	(3503 eliminated genes)

	 Level 3:	11 nodes to be scored	(4460 eliminated genes)

	 Level 2:	5 nodes to be scored	(5216 eliminated genes)

	 Level 1:	1 nodes to be scored	(5352 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 254 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	2 nodes to be scored	(0 eliminated genes)

	 Level 13:	1 nodes to be scored	(27 eliminated genes)

	 Level 12:	2 nodes to be scored	(98 eliminated genes)

	 Level 11:	7 nodes to be scored	(154 eliminated genes)

	 Level 10:	13 nodes to be scored	(286 eliminated genes)

	 Level 9:	21 nodes to be scored	(866 eliminated genes)

	 Level 8:	27 nodes to be scored	(1237 eliminated genes)

	 Level 7:	31 nodes to be scored	(1548 eliminated genes)

	 Level 6:	43 nodes to be scored	(2261 eliminated genes)

	 Level 5:	43 nodes to be scored	(2860 eliminated genes)

	 Level 4:	33 nodes to be scored	(4157 eliminated genes)

	 Level 3:	20 nodes to be scored	(4909 eliminated genes)

	 Level 2:	9 nodes to be scored	(5325 eliminated genes)

	 Level 1:	1 nodes to be scored	(5559 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 16 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 8:	1 nodes to be scored	(0 eliminated genes)

	 Level 7:	1 nodes to be scored	(0 eliminated genes)

	 Level 6:	1 nodes to be scored	(4 eliminated genes)

	 Level 5:	1 nodes to be scored	(36 eliminated genes)

	 Level 4:	2 nodes to be scored	(224 eliminated genes)

	 Level 3:	4 nodes to be scored	(342 eliminated genes)

	 Level 2:	5 nodes to be scored	(1628 eliminated genes)

	 Level 1:	1 nodes to be scored	(3624 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 226 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	4 nodes to be scored	(0 eliminated genes)

	 Level 12:	7 nodes to be scored	(0 eliminated genes)

	 Level 11:	12 nodes to be scored	(16 eliminated genes)

	 Level 10:	15 nodes to be scored	(373 eliminated genes)

	 Level 9:	18 nodes to be scored	(858 eliminated genes)

	 Level 8:	16 nodes to be scored	(970 eliminated genes)

	 Level 7:	22 nodes to be scored	(1375 eliminated genes)

	 Level 6:	36 nodes to be scored	(2358 eliminated genes)

	 Level 5:	41 nodes to be scored	(2709 eliminated genes)

	 Level 4:	28 nodes to be scored	(3638 eliminated genes)

	 Level 3:	19 nodes to be scored	(4572 eliminated genes)

	 Level 2:	7 nodes to be scored	(5067 eliminated genes)

	 Level 1:	1 nodes to be scored	(5505 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 178 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	5 nodes to be scored	(0 eliminated genes)

	 Level 10:	6 nodes to be scored	(327 eliminated genes)

	 Level 9:	13 nodes to be scored	(767 eliminated genes)

	 Level 8:	13 nodes to be scored	(850 eliminated genes)

	 Level 7:	19 nodes to be scored	(1028 eliminated genes)

	 Level 6:	30 nodes to be scored	(1610 eliminated genes)

	 Level 5:	36 nodes to be scored	(2652 eliminated genes)

	 Level 4:	28 nodes to be scored	(3995 eliminated genes)

	 Level 3:	18 nodes to be scored	(4726 eliminated genes)

	 Level 2:	7 nodes to be scored	(5240 eliminated genes)

	 Level 1:	1 nodes to be scored	(5523 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 199 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	3 nodes to be scored	(0 eliminated genes)

	 Level 11:	6 nodes to be scored	(4 eliminated genes)

	 Level 10:	15 nodes to be scored	(27 eliminated genes)

	 Level 9:	18 nodes to be scored	(200 eliminated genes)

	 Level 8:	17 nodes to be scored	(441 eliminated genes)

	 Level 7:	19 nodes to be scored	(641 eliminated genes)

	 Level 6:	23 nodes to be scored	(1082 eliminated genes)

	 Level 5:	37 nodes to be scored	(1692 eliminated genes)

	 Level 4:	33 nodes to be scored	(3282 eliminated genes)

	 Level 3:	19 nodes to be scored	(4698 eliminated genes)

	 Level 2:	7 nodes to be scored	(5301 eliminated genes)

	 Level 1:	1 nodes to be scored	(5555 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 297 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 14:	2 nodes to be scored	(0 eliminated genes)

	 Level 13:	8 nodes to be scored	(0 eliminated genes)

	 Level 12:	13 nodes to be scored	(20 eliminated genes)

	 Level 11:	18 nodes to be scored	(93 eliminated genes)

	 Level 10:	24 nodes to be scored	(267 eliminated genes)

	 Level 9:	36 nodes to be scored	(437 eliminated genes)

	 Level 8:	26 nodes to be scored	(923 eliminated genes)

	 Level 7:	21 nodes to be scored	(1324 eliminated genes)

	 Level 6:	31 nodes to be scored	(2032 eliminated genes)

	 Level 5:	52 nodes to be scored	(3031 eliminated genes)

	 Level 4:	38 nodes to be scored	(4274 eliminated genes)

	 Level 3:	19 nodes to be scored	(4973 eliminated genes)

	 Level 2:	8 nodes to be scored	(5414 eliminated genes)

	 Level 1:	1 nodes to be scored	(5558 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 84 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	3 nodes to be scored	(0 eliminated genes)

	 Level 11:	4 nodes to be scored	(0 eliminated genes)

	 Level 10:	6 nodes to be scored	(56 eliminated genes)

	 Level 9:	7 nodes to be scored	(115 eliminated genes)

	 Level 8:	5 nodes to be scored	(163 eliminated genes)

	 Level 7:	7 nodes to be scored	(242 eliminated genes)

	 Level 6:	9 nodes to be scored	(453 eliminated genes)

	 Level 5:	14 nodes to be scored	(568 eliminated genes)

	 Level 4:	15 nodes to be scored	(834 eliminated genes)

	 Level 3:	8 nodes to be scored	(3352 eliminated genes)

	 Level 2:	5 nodes to be scored	(4552 eliminated genes)

	 Level 1:	1 nodes to be scored	(5440 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 80 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	4 nodes to be scored	(0 eliminated genes)

	 Level 11:	4 nodes to be scored	(48 eliminated genes)

	 Level 10:	4 nodes to be scored	(118 eliminated genes)

	 Level 9:	4 nodes to be scored	(763 eliminated genes)

	 Level 8:	5 nodes to be scored	(793 eliminated genes)

	 Level 7:	4 nodes to be scored	(838 eliminated genes)

	 Level 6:	11 nodes to be scored	(930 eliminated genes)

	 Level 5:	18 nodes to be scored	(2139 eliminated genes)

	 Level 4:	11 nodes to be scored	(3348 eliminated genes)

	 Level 3:	9 nodes to be scored	(3707 eliminated genes)

	 Level 2:	4 nodes to be scored	(4297 eliminated genes)

	 Level 1:	1 nodes to be scored	(4918 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 102 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	2 nodes to be scored	(0 eliminated genes)

	 Level 12:	2 nodes to be scored	(86 eliminated genes)

	 Level 11:	4 nodes to be scored	(155 eliminated genes)

	 Level 10:	5 nodes to be scored	(286 eliminated genes)

	 Level 9:	5 nodes to be scored	(734 eliminated genes)

	 Level 8:	9 nodes to be scored	(800 eliminated genes)

	 Level 7:	9 nodes to be scored	(842 eliminated genes)

	 Level 6:	16 nodes to be scored	(1016 eliminated genes)

	 Level 5:	20 nodes to be scored	(2353 eliminated genes)

	 Level 4:	13 nodes to be scored	(3165 eliminated genes)

	 Level 3:	10 nodes to be scored	(3612 eliminated genes)

	 Level 2:	5 nodes to be scored	(4618 eliminated genes)

	 Level 1:	1 nodes to be scored	(5125 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 42 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 11:	1 nodes to be scored	(0 eliminated genes)

	 Level 10:	1 nodes to be scored	(0 eliminated genes)

	 Level 9:	4 nodes to be scored	(1 eliminated genes)

	 Level 8:	4 nodes to be scored	(4 eliminated genes)

	 Level 7:	4 nodes to be scored	(25 eliminated genes)

	 Level 6:	4 nodes to be scored	(278 eliminated genes)

	 Level 5:	5 nodes to be scored	(473 eliminated genes)

	 Level 4:	8 nodes to be scored	(516 eliminated genes)

	 Level 3:	7 nodes to be scored	(1176 eliminated genes)

	 Level 2:	3 nodes to be scored	(2543 eliminated genes)

	 Level 1:	1 nodes to be scored	(4939 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 248 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	2 nodes to be scored	(0 eliminated genes)

	 Level 14:	3 nodes to be scored	(0 eliminated genes)

	 Level 13:	4 nodes to be scored	(28 eliminated genes)

	 Level 12:	7 nodes to be scored	(45 eliminated genes)

	 Level 11:	11 nodes to be scored	(49 eliminated genes)

	 Level 10:	10 nodes to be scored	(131 eliminated genes)

	 Level 9:	21 nodes to be scored	(967 eliminated genes)

	 Level 8:	29 nodes to be scored	(1140 eliminated genes)

	 Level 7:	28 nodes to be scored	(1238 eliminated genes)

	 Level 6:	42 nodes to be scored	(1585 eliminated genes)

	 Level 5:	40 nodes to be scored	(2683 eliminated genes)

	 Level 4:	27 nodes to be scored	(3668 eliminated genes)

	 Level 3:	16 nodes to be scored	(4235 eliminated genes)

	 Level 2:	7 nodes to be scored	(4829 eliminated genes)

	 Level 1:	1 nodes to be scored	(5226 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 43 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 9:	1 nodes to be scored	(0 eliminated genes)

	 Level 8:	1 nodes to be scored	(0 eliminated genes)

	 Level 7:	1 nodes to be scored	(171 eliminated genes)

	 Level 6:	5 nodes to be scored	(762 eliminated genes)

	 Level 5:	10 nodes to be scored	(766 eliminated genes)

	 Level 4:	10 nodes to be scored	(2419 eliminated genes)

	 Level 3:	9 nodes to be scored	(3706 eliminated genes)

	 Level 2:	5 nodes to be scored	(4972 eliminated genes)

	 Level 1:	1 nodes to be scored	(5346 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 103 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	1 nodes to be scored	(12 eliminated genes)

	 Level 10:	3 nodes to be scored	(13 eliminated genes)

	 Level 9:	6 nodes to be scored	(14 eliminated genes)

	 Level 8:	8 nodes to be scored	(63 eliminated genes)

	 Level 7:	14 nodes to be scored	(320 eliminated genes)

	 Level 6:	18 nodes to be scored	(1118 eliminated genes)

	 Level 5:	21 nodes to be scored	(2250 eliminated genes)

	 Level 4:	13 nodes to be scored	(3306 eliminated genes)

	 Level 3:	11 nodes to be scored	(4578 eliminated genes)

	 Level 2:	5 nodes to be scored	(4964 eliminated genes)

	 Level 1:	1 nodes to be scored	(5371 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 151 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	2 nodes to be scored	(0 eliminated genes)

	 Level 12:	4 nodes to be scored	(0 eliminated genes)

	 Level 11:	5 nodes to be scored	(27 eliminated genes)

	 Level 10:	5 nodes to be scored	(462 eliminated genes)

	 Level 9:	8 nodes to be scored	(786 eliminated genes)

	 Level 8:	8 nodes to be scored	(845 eliminated genes)

	 Level 7:	11 nodes to be scored	(894 eliminated genes)

	 Level 6:	23 nodes to be scored	(1208 eliminated genes)

	 Level 5:	32 nodes to be scored	(2394 eliminated genes)

	 Level 4:	23 nodes to be scored	(3527 eliminated genes)

	 Level 3:	19 nodes to be scored	(4087 eliminated genes)

	 Level 2:	10 nodes to be scored	(4604 eliminated genes)

	 Level 1:	1 nodes to be scored	(5219 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 155 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	3 nodes to be scored	(5 eliminated genes)

	 Level 10:	4 nodes to be scored	(10 eliminated genes)

	 Level 9:	7 nodes to be scored	(72 eliminated genes)

	 Level 8:	8 nodes to be scored	(178 eliminated genes)

	 Level 7:	10 nodes to be scored	(687 eliminated genes)

	 Level 6:	23 nodes to be scored	(1948 eliminated genes)

	 Level 5:	36 nodes to be scored	(2798 eliminated genes)

	 Level 4:	31 nodes to be scored	(3672 eliminated genes)

	 Level 3:	20 nodes to be scored	(4744 eliminated genes)

	 Level 2:	10 nodes to be scored	(5218 eliminated genes)

	 Level 1:	1 nodes to be scored	(5522 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 230 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	2 nodes to be scored	(14 eliminated genes)

	 Level 12:	3 nodes to be scored	(42 eliminated genes)

	 Level 11:	7 nodes to be scored	(313 eliminated genes)

	 Level 10:	15 nodes to be scored	(509 eliminated genes)

	 Level 9:	21 nodes to be scored	(810 eliminated genes)

	 Level 8:	25 nodes to be scored	(1032 eliminated genes)

	 Level 7:	32 nodes to be scored	(1434 eliminated genes)

	 Level 6:	36 nodes to be scored	(1865 eliminated genes)

	 Level 5:	36 nodes to be scored	(2351 eliminated genes)

	 Level 4:	29 nodes to be scored	(3459 eliminated genes)

	 Level 3:	15 nodes to be scored	(4273 eliminated genes)

	 Level 2:	6 nodes to be scored	(4916 eliminated genes)

	 Level 1:	1 nodes to be scored	(5463 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 162 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	2 nodes to be scored	(0 eliminated genes)

	 Level 12:	3 nodes to be scored	(0 eliminated genes)

	 Level 11:	6 nodes to be scored	(272 eliminated genes)

	 Level 10:	8 nodes to be scored	(462 eliminated genes)

	 Level 9:	11 nodes to be scored	(754 eliminated genes)

	 Level 8:	13 nodes to be scored	(794 eliminated genes)

	 Level 7:	16 nodes to be scored	(856 eliminated genes)

	 Level 6:	27 nodes to be scored	(1107 eliminated genes)

	 Level 5:	30 nodes to be scored	(2222 eliminated genes)

	 Level 4:	24 nodes to be scored	(3484 eliminated genes)

	 Level 3:	14 nodes to be scored	(4184 eliminated genes)

	 Level 2:	7 nodes to be scored	(4730 eliminated genes)

	 Level 1:	1 nodes to be scored	(5198 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 119 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 14:	3 nodes to be scored	(0 eliminated genes)

	 Level 13:	2 nodes to be scored	(0 eliminated genes)

	 Level 12:	4 nodes to be scored	(56 eliminated genes)

	 Level 11:	7 nodes to be scored	(82 eliminated genes)

	 Level 10:	5 nodes to be scored	(268 eliminated genes)

	 Level 9:	8 nodes to be scored	(291 eliminated genes)

	 Level 8:	8 nodes to be scored	(544 eliminated genes)

	 Level 7:	9 nodes to be scored	(712 eliminated genes)

	 Level 6:	14 nodes to be scored	(837 eliminated genes)

	 Level 5:	20 nodes to be scored	(2152 eliminated genes)

	 Level 4:	18 nodes to be scored	(3597 eliminated genes)

	 Level 3:	13 nodes to be scored	(4091 eliminated genes)

	 Level 2:	7 nodes to be scored	(4395 eliminated genes)

	 Level 1:	1 nodes to be scored	(5199 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 261 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	5 nodes to be scored	(2 eliminated genes)

	 Level 10:	10 nodes to be scored	(10 eliminated genes)

	 Level 9:	17 nodes to be scored	(753 eliminated genes)

	 Level 8:	24 nodes to be scored	(1000 eliminated genes)

	 Level 7:	34 nodes to be scored	(1527 eliminated genes)

	 Level 6:	50 nodes to be scored	(2305 eliminated genes)

	 Level 5:	53 nodes to be scored	(3633 eliminated genes)

	 Level 4:	36 nodes to be scored	(4243 eliminated genes)

	 Level 3:	20 nodes to be scored	(4940 eliminated genes)

	 Level 2:	8 nodes to be scored	(5240 eliminated genes)

	 Level 1:	1 nodes to be scored	(5539 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 113 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	3 nodes to be scored	(0 eliminated genes)

	 Level 12:	6 nodes to be scored	(0 eliminated genes)

	 Level 11:	5 nodes to be scored	(61 eliminated genes)

	 Level 10:	3 nodes to be scored	(491 eliminated genes)

	 Level 9:	3 nodes to be scored	(765 eliminated genes)

	 Level 8:	4 nodes to be scored	(784 eliminated genes)

	 Level 7:	10 nodes to be scored	(791 eliminated genes)

	 Level 6:	18 nodes to be scored	(822 eliminated genes)

	 Level 5:	23 nodes to be scored	(1698 eliminated genes)

	 Level 4:	17 nodes to be scored	(3040 eliminated genes)

	 Level 3:	13 nodes to be scored	(4435 eliminated genes)

	 Level 2:	7 nodes to be scored	(5154 eliminated genes)

	 Level 1:	1 nodes to be scored	(5406 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 255 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	4 nodes to be scored	(13 eliminated genes)

	 Level 12:	8 nodes to be scored	(32 eliminated genes)

	 Level 11:	11 nodes to be scored	(391 eliminated genes)

	 Level 10:	13 nodes to be scored	(745 eliminated genes)

	 Level 9:	24 nodes to be scored	(1119 eliminated genes)

	 Level 8:	24 nodes to be scored	(1332 eliminated genes)

	 Level 7:	33 nodes to be scored	(1474 eliminated genes)

	 Level 6:	38 nodes to be scored	(2408 eliminated genes)

	 Level 5:	43 nodes to be scored	(3336 eliminated genes)

	 Level 4:	33 nodes to be scored	(4192 eliminated genes)

	 Level 3:	15 nodes to be scored	(4800 eliminated genes)

	 Level 2:	6 nodes to be scored	(5361 eliminated genes)

	 Level 1:	1 nodes to be scored	(5500 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 1 nontrivial nodes
		 parameters: 
			 test statistic: fisher
Nothing to do:
Nothing to do:

	 Level 1:	1 nodes to be scored	(0 eliminated genes)
Warning message in .genesInNode(graph(object), whichGO):
“Nodes not present in the graph:NA”
Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 87 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	2 nodes to be scored	(0 eliminated genes)

	 Level 10:	4 nodes to be scored	(426 eliminated genes)

	 Level 9:	5 nodes to be scored	(752 eliminated genes)

	 Level 8:	5 nodes to be scored	(785 eliminated genes)

	 Level 7:	4 nodes to be scored	(786 eliminated genes)

	 Level 6:	11 nodes to be scored	(920 eliminated genes)

	 Level 5:	20 nodes to be scored	(1776 eliminated genes)

	 Level 4:	16 nodes to be scored	(2843 eliminated genes)

	 Level 3:	12 nodes to be scored	(3831 eliminated genes)

	 Level 2:	6 nodes to be scored	(4270 eliminated genes)

	 Level 1:	1 nodes to be scored	(5040 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 261 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 14:	2 nodes to be scored	(0 eliminated genes)

	 Level 13:	2 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(36 eliminated genes)

	 Level 11:	8 nodes to be scored	(389 eliminated genes)

	 Level 10:	12 nodes to be scored	(557 eliminated genes)

	 Level 9:	22 nodes to be scored	(775 eliminated genes)

	 Level 8:	28 nodes to be scored	(850 eliminated genes)

	 Level 7:	31 nodes to be scored	(1096 eliminated genes)

	 Level 6:	41 nodes to be scored	(1682 eliminated genes)

	 Level 5:	48 nodes to be scored	(2820 eliminated genes)

	 Level 4:	32 nodes to be scored	(4098 eliminated genes)

	 Level 3:	20 nodes to be scored	(4905 eliminated genes)

	 Level 2:	9 nodes to be scored	(5348 eliminated genes)

	 Level 1:	1 nodes to be scored	(5555 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 270 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 16:	1 nodes to be scored	(0 eliminated genes)

	 Level 15:	3 nodes to be scored	(0 eliminated genes)

	 Level 14:	4 nodes to be scored	(4 eliminated genes)

	 Level 13:	3 nodes to be scored	(14 eliminated genes)

	 Level 12:	5 nodes to be scored	(49 eliminated genes)

	 Level 11:	6 nodes to be scored	(295 eliminated genes)

	 Level 10:	12 nodes to be scored	(479 eliminated genes)

	 Level 9:	15 nodes to be scored	(799 eliminated genes)

	 Level 8:	17 nodes to be scored	(910 eliminated genes)

	 Level 7:	26 nodes to be scored	(1110 eliminated genes)

	 Level 6:	43 nodes to be scored	(1954 eliminated genes)

	 Level 5:	56 nodes to be scored	(3392 eliminated genes)

	 Level 4:	45 nodes to be scored	(4124 eliminated genes)

	 Level 3:	23 nodes to be scored	(4855 eliminated genes)

	 Level 2:	10 nodes to be scored	(5331 eliminated genes)

	 Level 1:	1 nodes to be scored	(5542 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 139 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(0 eliminated genes)

	 Level 11:	10 nodes to be scored	(48 eliminated genes)

	 Level 10:	15 nodes to be scored	(119 eliminated genes)

	 Level 9:	16 nodes to be scored	(821 eliminated genes)

	 Level 8:	12 nodes to be scored	(948 eliminated genes)

	 Level 7:	7 nodes to be scored	(1030 eliminated genes)

	 Level 6:	16 nodes to be scored	(1160 eliminated genes)

	 Level 5:	24 nodes to be scored	(2365 eliminated genes)

	 Level 4:	17 nodes to be scored	(3512 eliminated genes)

	 Level 3:	10 nodes to be scored	(3917 eliminated genes)

	 Level 2:	5 nodes to be scored	(4531 eliminated genes)

	 Level 1:	1 nodes to be scored	(5159 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 185 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	4 nodes to be scored	(0 eliminated genes)

	 Level 12:	6 nodes to be scored	(0 eliminated genes)

	 Level 11:	8 nodes to be scored	(361 eliminated genes)

	 Level 10:	9 nodes to be scored	(579 eliminated genes)

	 Level 9:	9 nodes to be scored	(756 eliminated genes)

	 Level 8:	12 nodes to be scored	(857 eliminated genes)

	 Level 7:	20 nodes to be scored	(902 eliminated genes)

	 Level 6:	30 nodes to be scored	(1344 eliminated genes)

	 Level 5:	33 nodes to be scored	(2677 eliminated genes)

	 Level 4:	27 nodes to be scored	(3577 eliminated genes)

	 Level 3:	17 nodes to be scored	(4020 eliminated genes)

	 Level 2:	9 nodes to be scored	(4800 eliminated genes)

	 Level 1:	1 nodes to be scored	(5198 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 272 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 16:	1 nodes to be scored	(0 eliminated genes)

	 Level 15:	2 nodes to be scored	(0 eliminated genes)

	 Level 14:	2 nodes to be scored	(5 eliminated genes)

	 Level 13:	6 nodes to be scored	(37 eliminated genes)

	 Level 12:	8 nodes to be scored	(98 eliminated genes)

	 Level 11:	10 nodes to be scored	(440 eliminated genes)

	 Level 10:	13 nodes to be scored	(578 eliminated genes)

	 Level 9:	20 nodes to be scored	(929 eliminated genes)

	 Level 8:	23 nodes to be scored	(1087 eliminated genes)

	 Level 7:	28 nodes to be scored	(1241 eliminated genes)

	 Level 6:	41 nodes to be scored	(1811 eliminated genes)

	 Level 5:	46 nodes to be scored	(2899 eliminated genes)

	 Level 4:	40 nodes to be scored	(4041 eliminated genes)

	 Level 3:	23 nodes to be scored	(4568 eliminated genes)

	 Level 2:	8 nodes to be scored	(5130 eliminated genes)

	 Level 1:	1 nodes to be scored	(5487 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 107 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	2 nodes to be scored	(26 eliminated genes)

	 Level 10:	5 nodes to be scored	(26 eliminated genes)

	 Level 9:	5 nodes to be scored	(35 eliminated genes)

	 Level 8:	9 nodes to be scored	(91 eliminated genes)

	 Level 7:	14 nodes to be scored	(181 eliminated genes)

	 Level 6:	15 nodes to be scored	(499 eliminated genes)

	 Level 5:	21 nodes to be scored	(888 eliminated genes)

	 Level 4:	15 nodes to be scored	(1865 eliminated genes)

	 Level 3:	12 nodes to be scored	(2638 eliminated genes)

	 Level 2:	6 nodes to be scored	(3710 eliminated genes)

	 Level 1:	1 nodes to be scored	(5501 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 106 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	1 nodes to be scored	(0 eliminated genes)

	 Level 10:	4 nodes to be scored	(17 eliminated genes)

	 Level 9:	5 nodes to be scored	(28 eliminated genes)

	 Level 8:	9 nodes to be scored	(133 eliminated genes)

	 Level 7:	12 nodes to be scored	(238 eliminated genes)

	 Level 6:	14 nodes to be scored	(658 eliminated genes)

	 Level 5:	24 nodes to be scored	(1384 eliminated genes)

	 Level 4:	17 nodes to be scored	(2594 eliminated genes)

	 Level 3:	12 nodes to be scored	(4507 eliminated genes)

	 Level 2:	6 nodes to be scored	(4870 eliminated genes)

	 Level 1:	1 nodes to be scored	(5456 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 102 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	1 nodes to be scored	(0 eliminated genes)

	 Level 10:	3 nodes to be scored	(9 eliminated genes)

	 Level 9:	4 nodes to be scored	(14 eliminated genes)

	 Level 8:	8 nodes to be scored	(34 eliminated genes)

	 Level 7:	12 nodes to be scored	(96 eliminated genes)

	 Level 6:	14 nodes to be scored	(204 eliminated genes)

	 Level 5:	17 nodes to be scored	(458 eliminated genes)

	 Level 4:	19 nodes to be scored	(845 eliminated genes)

	 Level 3:	13 nodes to be scored	(1849 eliminated genes)

	 Level 2:	9 nodes to be scored	(4470 eliminated genes)

	 Level 1:	1 nodes to be scored	(5420 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 99 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	1 nodes to be scored	(0 eliminated genes)

	 Level 10:	2 nodes to be scored	(54 eliminated genes)

	 Level 9:	4 nodes to be scored	(159 eliminated genes)

	 Level 8:	5 nodes to be scored	(276 eliminated genes)

	 Level 7:	10 nodes to be scored	(340 eliminated genes)

	 Level 6:	13 nodes to be scored	(786 eliminated genes)

	 Level 5:	19 nodes to be scored	(1383 eliminated genes)

	 Level 4:	17 nodes to be scored	(2788 eliminated genes)

	 Level 3:	18 nodes to be scored	(4530 eliminated genes)

	 Level 2:	8 nodes to be scored	(5068 eliminated genes)

	 Level 1:	1 nodes to be scored	(5558 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 27 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 8:	1 nodes to be scored	(0 eliminated genes)

	 Level 7:	1 nodes to be scored	(0 eliminated genes)

	 Level 6:	5 nodes to be scored	(9 eliminated genes)

	 Level 5:	5 nodes to be scored	(259 eliminated genes)

	 Level 4:	5 nodes to be scored	(2304 eliminated genes)

	 Level 3:	6 nodes to be scored	(3762 eliminated genes)

	 Level 2:	3 nodes to be scored	(4385 eliminated genes)

	 Level 1:	1 nodes to be scored	(4945 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 242 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	9 nodes to be scored	(0 eliminated genes)

	 Level 13:	12 nodes to be scored	(2 eliminated genes)

	 Level 12:	7 nodes to be scored	(11 eliminated genes)

	 Level 11:	5 nodes to be scored	(344 eliminated genes)

	 Level 10:	7 nodes to be scored	(556 eliminated genes)

	 Level 9:	9 nodes to be scored	(752 eliminated genes)

	 Level 8:	14 nodes to be scored	(789 eliminated genes)

	 Level 7:	32 nodes to be scored	(806 eliminated genes)

	 Level 6:	40 nodes to be scored	(994 eliminated genes)

	 Level 5:	45 nodes to be scored	(2144 eliminated genes)

	 Level 4:	34 nodes to be scored	(3377 eliminated genes)

	 Level 3:	17 nodes to be scored	(4292 eliminated genes)

	 Level 2:	9 nodes to be scored	(4872 eliminated genes)

	 Level 1:	1 nodes to be scored	(5205 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 94 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 11:	1 nodes to be scored	(0 eliminated genes)

	 Level 10:	2 nodes to be scored	(0 eliminated genes)

	 Level 9:	6 nodes to be scored	(6 eliminated genes)

	 Level 8:	6 nodes to be scored	(39 eliminated genes)

	 Level 7:	10 nodes to be scored	(165 eliminated genes)

	 Level 6:	9 nodes to be scored	(395 eliminated genes)

	 Level 5:	20 nodes to be scored	(749 eliminated genes)

	 Level 4:	17 nodes to be scored	(1301 eliminated genes)

	 Level 3:	14 nodes to be scored	(2288 eliminated genes)

	 Level 2:	8 nodes to be scored	(3423 eliminated genes)

	 Level 1:	1 nodes to be scored	(4616 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 132 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	6 nodes to be scored	(0 eliminated genes)

	 Level 10:	8 nodes to be scored	(10 eliminated genes)

	 Level 9:	10 nodes to be scored	(763 eliminated genes)

	 Level 8:	10 nodes to be scored	(894 eliminated genes)

	 Level 7:	8 nodes to be scored	(931 eliminated genes)

	 Level 6:	17 nodes to be scored	(1259 eliminated genes)

	 Level 5:	25 nodes to be scored	(2028 eliminated genes)

	 Level 4:	21 nodes to be scored	(3034 eliminated genes)

	 Level 3:	15 nodes to be scored	(3829 eliminated genes)

	 Level 2:	9 nodes to be scored	(4757 eliminated genes)

	 Level 1:	1 nodes to be scored	(5194 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 67 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	3 nodes to be scored	(149 eliminated genes)

	 Level 10:	3 nodes to be scored	(529 eliminated genes)

	 Level 9:	3 nodes to be scored	(752 eliminated genes)

	 Level 8:	3 nodes to be scored	(784 eliminated genes)

	 Level 7:	6 nodes to be scored	(785 eliminated genes)

	 Level 6:	11 nodes to be scored	(845 eliminated genes)

	 Level 5:	15 nodes to be scored	(1625 eliminated genes)

	 Level 4:	10 nodes to be scored	(2722 eliminated genes)

	 Level 3:	6 nodes to be scored	(3525 eliminated genes)

	 Level 2:	3 nodes to be scored	(4075 eliminated genes)

	 Level 1:	1 nodes to be scored	(4344 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 204 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	6 nodes to be scored	(19 eliminated genes)

	 Level 10:	14 nodes to be scored	(21 eliminated genes)

	 Level 9:	19 nodes to be scored	(311 eliminated genes)

	 Level 8:	15 nodes to be scored	(447 eliminated genes)

	 Level 7:	20 nodes to be scored	(606 eliminated genes)

	 Level 6:	27 nodes to be scored	(933 eliminated genes)

	 Level 5:	35 nodes to be scored	(1168 eliminated genes)

	 Level 4:	34 nodes to be scored	(3708 eliminated genes)

	 Level 3:	21 nodes to be scored	(5012 eliminated genes)

	 Level 2:	10 nodes to be scored	(5297 eliminated genes)

	 Level 1:	1 nodes to be scored	(5526 eliminated genes)

Building most specific GOs .....
	( 2909 GO terms found. )

Build GO DAG topology ..........
	( 5064 GO terms and 11404 relations. )

Annotating nodes ...............
	( 6419 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 75 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 12:	2 nodes to be scored	(0 eliminated genes)

	 Level 11:	2 nodes to be scored	(0 eliminated genes)

	 Level 10:	3 nodes to be scored	(47 eliminated genes)

	 Level 9:	5 nodes to be scored	(99 eliminated genes)

	 Level 8:	5 nodes to be scored	(152 eliminated genes)

	 Level 7:	8 nodes to be scored	(186 eliminated genes)

	 Level 6:	9 nodes to be scored	(456 eliminated genes)

	 Level 5:	14 nodes to be scored	(752 eliminated genes)

	 Level 4:	14 nodes to be scored	(1291 eliminated genes)

	 Level 3:	7 nodes to be scored	(3335 eliminated genes)

	 Level 2:	5 nodes to be scored	(4503 eliminated genes)

	 Level 1:	1 nodes to be scored	(5252 eliminated genes)

In [15]:

    

rownames(enrichmentResults) <- c("terms","p-values","genes")
colnames(enrichmentResults) <- 1:max(assignments)


    

In [17]:

    

enrichmentResults["terms",]


    

    






	
$`1`
		

go_id
Term
Definition

	
131
GO:0000050                                                                                                                                                                                                                                                                                                                                                                                                                                                  
urea cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.                                                                                                                                                                                         
	
137
GO:0000053                                                                                                                                                                                                                                                                                                                                                                                                                                                  
argininosuccinate metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate.                                                                                                                                                                                                                                                        
	
335
GO:0000132                                                                                                                                                                                                                                                                                                                                                                                                                                                  
establishment of mitotic spindle orientation                                                                                                                                                                                                                                                                                                                                                                                                                
A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.                                                                                                                                                                                                                                                                                                                                                      
	
459
GO:0000184                                                                                                                                                                                                                                                                                                                                                                                                                                                  
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay                                                                                                                                                                                                                                                                                                                                                                                         
The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.                                                                                                                                                                                                               
	
834
GO:0000288                                                                                                                                                                                                                                                                                                                                                                                                                                                  
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                                                                                                                                                                                                                                                                   
A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.                                                                                                                                                                                                                                                                     
	
845
GO:0000290                                                                                                                                                                                                                                                                                                                                                                                                                                                  
deadenylation-dependent decapping of nuclear-transcribed mRNA                                                                                                                                                                                                                                                                                                                                                                                               
Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.                                                                                                                                                                                                                                                                                                                                  
	
1129
GO:0000422                                                                                                                                                                                                                                                                                                                                                                                                                                                  
mitophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.                                                                                                                                                                                                                                                                                                                         
	
1247
GO:0000706                                                                                                                                                                                                                                                                                                                                                                                                                                                  
meiotic DNA double-strand break processing                                                                                                                                                                                                                                                                                                                                                                                                                  
The cell cycle process in which the 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang occurs. This takes place during meiosis.                                                                                                                                                                                                                                                                  
	
1282
GO:0000722                                                                                                                                                                                                                                                                                                                                                                                                                                                  
telomere maintenance via recombination                                                                                                                                                                                                                                                                                                                                                                                                                      
Any recombinational process that contributes to the maintenance of proper telomeric length.                                                                                                                                                                                                                                                                                                                                                                 
	
1283
GO:0000723                                                                                                                                                                                                                                                                                                                                                                                                                                                  
telomere maintenance                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.                                                                                                                    
	
1296
GO:0000730                                                                                                                                                                                                                                                                                                                                                                                                                                                  
DNA recombinase assembly                                                                                                                                                                                                                                                                                                                                                                                                                                    
The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.                                                                                                                                                                                                                                                                                                            
	
1718
GO:0001081                                                                                                                                                                                                                                                                                                                                                                                                                                                  
nitrogen catabolite repression of transcription from RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                             
A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.                                                                                                                                                                                         
	
1737
GO:0001100                                                                                                                                                                                                                                                                                                                                                                                                                                                  
negative regulation of exit from mitosis                                                                                                                                                                                                                                                                                                                                                                                                                    
Any process involved in the inhibition of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).                                                                                                                                                                                                                                                                                                                 
	
2134
GO:0001558                                                                                                                                                                                                                                                                                                                                                                                                                                                  
regulation of cell growth                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any process that modulates the frequency, rate, extent or direction of cell growth.                                                                                                                                                                                                                                                                                                                                                                         
	
6237
GO:0051017                                                                                                                                                                                                                                                                                                                                                                                                                                                  
actin filament bundle assembly                                                                                                                                                                                                                                                                                                                                                                                                                              
The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.                                                                                                                                                                                                                                                                 
	
15257
GO:0006279                                                                                                                                                                                                                                                                                                                                                                                                                                                  
premeiotic DNA replication                                                                                                                                                                                                                                                                                                                                                                                                                                  
The replication of DNA that precedes meiotic cell division.                                                                                                                                                                                                                                                                                                                                                                                                 
	
15538
GO:0006468                                                                                                                                                                                                                                                                                                                                                                                                                                                  
protein phosphorylation                                                                                                                                                                                                                                                                                                                                                                                                                                     
The process of introducing a phosphate group on to a protein.                                                                                                                                                                                                                                                                                                                                                                                               
	
15892
GO:0006607                                                                                                                                                                                                                                                                                                                                                                                                                                                  
NLS-bearing protein import into nucleus                                                                                                                                                                                                                                                                                                                                                                                                                     
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.                                                                                                                                                                                                                                                                                                            
	
16709
GO:0006913                                                                                                                                                                                                                                                                                                                                                                                                                                                  
nucleocytoplasmic transport                                                                                                                                                                                                                                                                                                                                                                                                                                 
The directed movement of molecules between the nucleus and the cytoplasm.                                                                                                                                                                                                                                                                                                                                                                                   
	
16856
GO:0006995                                                                                                                                                                                                                                                                                                                                                                                                                                                  
cellular response to nitrogen starvation                                                                                                                                                                                                                                                                                                                                                                                                                    
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.                                                                                                                                                                                                                                                                     
	
16867
GO:0006999                                                                                                                                                                                                                                                                                                                                                                                                                                                  
nuclear pore organization                                                                                                                                                                                                                                                                                                                                                                                                                                   
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.                                                                                                                                                                                                                                                                                                    
	
16942
GO:0007049                                                                                                                                                                                                                                                                                                                                                                                                                                                  
cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.                                                
	
16968
GO:0007067                                                                                                                                                                                                                                                                                                                                                                                                                                                  
mitotic nuclear division                                                                                                                                                                                                                                                                                                                                                                                                                                    
A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.                                                                                                                                                      
	
17027
GO:0007094                                                                                                                                                                                                                                                                                                                                                                                                                                                  
mitotic spindle assembly checkpoint                                                                                                                                                                                                                                                                                                                                                                                                                         
A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.                                                                                                                                                                                                                                                                   
	
19499
GO:0030041                                                                                                                                                                                                                                                                                                                                                                                                                                                  
actin filament polymerization                                                                                                                                                                                                                                                                                                                                                                                                                               
Assembly of actin filaments by the addition of actin monomers to a filament.                                                                                                                                                                                                                                                                                                                                                                                
	
23079
GO:0009847                                                                                                                                                                                                                                                                                                                                                                                                                                                  
spore germination                                                                                                                                                                                                                                                                                                                                                                                                                                           
The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall).                                                                                                                                                                                                                                                                                    
	
23814
GO:0010212                                                                                                                                                                                                                                                                                                                                                                                                                                                  
response to ionizing radiation                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
	
24353
GO:0010621                                                                                                                                                                                                                                                                                                                                                                                                                                                  
negative regulation of transcription by transcription factor localization                                                                                                                                                                                                                                                                                                                                                                                   
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor.                                                                                                                                                                                                                                                                       
	
24566
GO:0010791                                                                                                                                                                                                                                                                                                                                                                                                                                                  
DNA double-strand break processing involved in repair via synthesis-dependent strand annealing                                                                                                                                                                                                                                                                                                                                                              
The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang that results in the repair of a double strand break via synthesis-dependent strand annealing.                                                                                                                                                                                                                                             
	
26891
GO:0045722                                                                                                                                                                                                                                                                                                                                                                                                                                                  
positive regulation of gluconeogenesis                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that activates or increases the frequency, rate or extent of gluconeogenesis.                                                                                                                                                                                                                                                                                                                                                                   
	
⋮
⋮
⋮
⋮
	
54154
GO:0044774                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
mitotic DNA integrity checkpoint                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
A mitotic cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and ends with signal transduction.                                                                                                                                                                                                                                                   
	
54185
GO:0044805                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
late nucleophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.                                                                                                                                                                                                                                                                                                                                           
	
54302
GO:0070987                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
error-free translesion synthesis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
	
54648
GO:0045143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
homologous chromosome segregation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the first division of the meiotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner; this pairing off, referred to as synapsis, permits genetic recombination. One homolog (both sister chromatids) of each morphologic type goes into each of the resulting chromosome sets.                                
	
55791
GO:0045429                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of nitric oxide biosynthetic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.                                                                                                                                                                                                                                                                                                                                                                                              
	
58376
GO:0046081                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
dUTP catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.                                                                                                                                                                                                                                                                                                                                                                                                                                               
	
65071
GO:0048213                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Golgi vesicle prefusion complex stabilization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The binding of specific proteins to the t-SNARE/v-SNARE/SNAP25 complex, by which the Golgi vesicle prefusion complex is stabilized.                                                                                                                                                                                                                                                                                                                                                                                                                   
	
69682
GO:0051028                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
mRNA transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                                                                                     
	
69691
GO:0051037                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
regulation of transcription involved in meiotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Any process that modulates the frequency, rate or extent of transcription as part of a meiotic cell cycle.                                                                                                                                                                                                                                                                                                                                                                                                                                            
	
69919
GO:0051123                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
RNA polymerase II transcriptional preinitiation complex assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.                                                                                                                                                                                                                                                                                                             
	
70518
GO:0051292                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear pore complex assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.                                                                                                                                                                                                                                                                                                                                                                                                                                              
	
70542
GO:0051301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
cell division                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                                                                                                                                                                                                                                                                        
	
70564
GO:0051312                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
chromosome decondensation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The alteration of chromosome structure from the condensed form to a relaxed disperse form.                                                                                                                                                                                                                                                                                                                                                                                                                                                            
	
70937
GO:0051441                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of ubiquitin-protein ligase activity involved in meiotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Any process that activates, maintains or increases the rate of ubiquitin ligase activity during the meiotic cell cycle.                                                                                                                                                                                                                                                                                                                                                                                                                               
	
78651
GO:0070550                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
rDNA condensation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The process in which the chromatin structure of the rDNA repeats is compacted. In S. cerevisiae, condensation and resolution of the rDNA occurs during anaphase.                                                                                                                                                                                                                                                                                                                                                                                      
	
79446
GO:0070941                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
eisosome assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The aggregation, arrangement and bonding together of a set of components to form an eisosome, a cell part that is composed of the eisosome membrane or MCC domain, a furrow-like plasma membrane sub-domain and associated integral transmembrane proteins, and the proteins (eisosome filaments) that form a scaffolding lattice on the cytoplasmic face.                                                                                                                                                                                            
	
81159
GO:0071940                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
fungal-type cell wall assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The aggregation, arrangement and bonding together of a set of components to form a fungal-type cell wall.                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
82920
GO:0080009                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
mRNA methylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
83829
GO:0090368                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
regulation of ornithine metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.                                                                                                                                                                                                                                                     
	
87592
GO:1900152                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.                                                                                                                                                                                                                                                                                                                                                                                               
	
87636
GO:1900153                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.                                                                                                                                                                                                                                                                                                                                                                                                   
	
90493
GO:1900475                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                                                                
Any process that activates or increases the frequency, rate or extent of meiosis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                                                                                                                                                                                                                                                                                                              
	
90498
GO:1900476                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of meiosis by positive regulation of transcription from RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                                                                
Any process that activates or increases the frequency, rate or extent of meiosis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                                                                                                                                                                                                                                                                                                                       
	
96687
GO:1901300                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of hydrogen peroxide-mediated programmed cell death                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Any process that activates or increases the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.                                                                                                                                                                                                                                                                                                                                                                                                                            
	
111245
GO:1903343                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of meiotic DNA double-strand break formation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that activates or increases the frequency, rate or extent of meiotic DNA double-strand break formation.                                                                                                                                                                                                                                                                                                                                                                                                                                   
	
115186
GO:1903833                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of cellular response to amino acid starvation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
129962
GO:1990022                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
RNA polymerase III complex localization to nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
The directed movement of an RNA polymerase III complex from the cytoplasm to the nucleus.                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
131340
GO:2000042                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
negative regulation of double-strand break repair via homologous recombination                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process that stops, prevents, or reduces the frequency, rate or extent of double-strand break repair via homologous recombination.                                                                                                                                                                                                                                                                                                                                                                                                                
	
131765
GO:2000221                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
negative regulation of pseudohyphal growth                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Any process that stops, prevents, or reduces the frequency, rate or extent of pseudohyphal growth.                                                                                                                                                                                                                                                                                                                                                                                                                                                    
	
133559
GO:2001158                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of proline catabolic process to glutamate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Any process that activates or increases the frequency, rate or extent of proline catabolic process to glutamate.                                                                                                                                                                                                                                                                                                                                                                                                                                      



	
$`2`
		

go_id
Term
Definition

	
1074
GO:0000398                                                                                                                                                                                                                  
mRNA splicing, via spliceosome                                                                                                                                                                                              
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	
36049
GO:0031116                                                                                                                                                                                                                  
positive regulation of microtubule polymerization                                                                                                                                                                           
Any process that activates or increases the frequency, rate or extent of microtubule polymerization.                                                                                                                        
	
72658
GO:0051987                                                                                                                                                                                                                  
positive regulation of attachment of spindle microtubules to kinetochore                                                                                                                                                    
Any process that activates or increases the frequency, rate or extent of the attachment of spindle microtubules to the kinetochore.                                                                                         



	
$`3`
		

go_id
Term
Definition

	
1253
GO:0000709                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
meiotic joint molecule formation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The conversion of the paired broken DNA and homologous duplex DNA into a four-stranded branched intermediate, known as a joint molecule, formed during meiotic recombination. These joint molecules contain Holliday junctions on either side of heteroduplex DNA.                                                                                                                                                                                                                                                                                                                                                                                                         
	
1296
GO:0000730                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
DNA recombinase assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
2134
GO:0001558                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
regulation of cell growth                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Any process that modulates the frequency, rate, extent or direction of cell growth.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
	
6237
GO:0051017                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
actin filament bundle assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
	
8906
GO:0006915                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
apoptotic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	
14824
GO:0045454                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
cell redox homeostasis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Any process that maintains the redox environment of a cell or compartment within a cell.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
	
17067
GO:0007130                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
synaptonemal complex assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The cell cycle process in which the synaptonemal complex is formed. This is a structure that holds paired chromosomes together during prophase I of meiosis and that promotes genetic recombination.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
	
23814
GO:0010212                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
response to ionizing radiation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.                                                                                                                                                                                                               
	
27216
GO:0016197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
endosomal transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
27304
GO:0016226                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
iron-sulfur cluster assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
	
35727
GO:0030950                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
establishment or maintenance of actin cytoskeleton polarity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
Any cellular process that results in the specification, formation or maintenance of polarized actin-based cytoskeletal structures.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
	
37648
GO:0031929                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
TOR signaling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors.                                                                                                                                                                                                                                                                                                                                                                                                                      
	
38655
GO:0032366                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
intracellular sterol transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The directed movement of sterols within cells.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
47807
GO:0038203                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
TORC2 signaling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
A series of intracellular molecular signals mediated by TORC2; TOR (rapamycin-insensitive companion of TOR) in complex with at least Rictor (regulatory-associated protein of TOR), or orthologs of, and other signaling components.                                                                                                                                                                                                                                                                                                                                                                                                                                       
	
48683
GO:0042148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
strand invasion                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules.                                                                                                                                                                                                                                                                                     
	
79446
GO:0070941                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
eisosome assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
The aggregation, arrangement and bonding together of a set of components to form an eisosome, a cell part that is composed of the eisosome membrane or MCC domain, a furrow-like plasma membrane sub-domain and associated integral transmembrane proteins, and the proteins (eisosome filaments) that form a scaffolding lattice on the cytoplasmic face.                                                                                                                                                                                                                                                                                                                 
	
83423
GO:0090002                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
establishment of protein localization to plasma membrane                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The directed movement of a protein to a specific location in the plasma membrane.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          



	
$`4`
		

go_id
Term
Definition

	
842
GO:0000289                                                                                                                                                                                                                                                                                                                                                       
nuclear-transcribed mRNA poly(A) tail shortening                                                                                                                                                                                                                                                                                                                 
Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.                                                                                                                                                                                                                                                             
	
845
GO:0000290                                                                                                                                                                                                                                                                                                                                                       
deadenylation-dependent decapping of nuclear-transcribed mRNA                                                                                                                                                                                                                                                                                                    
Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.                                                                                                                                                                                                                                       
	
1187
GO:0000463                                                                                                                                                                                                                                                                                                                                                       
maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)                                                                                                                                                                                                                                                                         
Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.
	
1340
GO:0000749                                                                                                                                                                                                                                                                                                                                                       
response to pheromone involved in conjugation with cellular fusion                                                                                                                                                                                                                                                                                               
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus that contributes to the process of conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae.                         
	
2001
GO:0001402                                                                                                                                                                                                                                                                                                                                                       
signal transduction involved in filamentous growth                                                                                                                                                                                                                                                                                                               
Relaying of environmental signals promoting filamentous growth.                                                                                                                                                                                                                                                                                                  
	
16799
GO:0006972                                                                                                                                                                                                                                                                                                                                                       
hyperosmotic response                                                                                                                                                                                                                                                                                                                                            
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.                                    
	
17047
GO:0030010                                                                                                                                                                                                                                                                                                                                                       
establishment of cell polarity                                                                                                                                                                                                                                                                                                                                   
The specification and formation of anisotropic intracellular organization or cell growth patterns.                                                                                                                                                                                                                                                               
	
17330
GO:0007232                                                                                                                                                                                                                                                                                                                                                       
osmosensory signaling pathway via Sho1 osmosensor                                                                                                                                                                                                                                                                                                                
A series of molecular signals generated in response to osmotic change, as mediated through a Sho1 osmosensor system.                                                                                                                                                                                                                                             
	
28775
GO:0017148                                                                                                                                                                                                                                                                                                                                                       
negative regulation of translation                                                                                                                                                                                                                                                                                                                               
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.                                                                                                                                                                             
	
36000
GO:0031087                                                                                                                                                                                                                                                                                                                                                       
deadenylation-independent decapping of nuclear-transcribed mRNA                                                                                                                                                                                                                                                                                                  
Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.                                                                                                                                                                                                                                                             
	
40371
GO:0032968                                                                                                                                                                                                                                                                                                                                                       
positive regulation of transcription elongation from RNA polymerase II promoter                                                                                                                                                                                                                                                                                  
Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.                                                                                                    
	
49037
GO:0042255                                                                                                                                                                                                                                                                                                                                                       
ribosome assembly                                                                                                                                                                                                                                                                                                                                                
The aggregation, arrangement and bonding together of the mature ribosome and of its subunits.                                                                                                                                                                                                                                                                    
	
105084
GO:1902626                                                                                                                                                                                                                                                                                                                                                       
assembly of large subunit precursor of preribosome                                                                                                                                                                                                                                                                                                               
The aggregation, arrangement and bonding together of a set of components to form the large subunit precursor of the preribosome.                                                                                                                                                                                                                                 



	
$`5`
		

go_id
Term
Definition

	
1597
GO:0000973                                                                                                                                                                                                                                                                                                                                                                                                                                    
posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery                                                                                                                                                                                                                                                                                                                                                              
The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.                                                                                                                                                                                                                   
	
14747
GO:0006094                                                                                                                                                                                                                                                                                                                                                                                                                                    
gluconeogenesis                                                                                                                                                                                                                                                                                                                                                                                                                               
The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.                                                                                                                                                                                                                                                                                                                                         
	
14749
GO:0006096                                                                                                                                                                                                                                                                                                                                                                                                                                    
glycolytic process                                                                                                                                                                                                                                                                                                                                                                                                                            
The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	
14757
GO:0006098                                                                                                                                                                                                                                                                                                                                                                                                                                    
pentose-phosphate shunt                                                                                                                                                                                                                                                                                                                                                                                                                       
The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.             
	
23346
GO:0009968                                                                                                                                                                                                                                                                                                                                                                                                                                    
negative regulation of signal transduction                                                                                                                                                                                                                                                                                                                                                                                                    
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.                                                                                                                                                                                                                                                                                                                                            
	
34090
GO:0030242                                                                                                                                                                                                                                                                                                                                                                                                                                    
pexophagy                                                                                                                                                                                                                                                                                                                                                                                                                                     
The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions.                                                                                                                                                                                                                                                                                                                       
	
44014
GO:0034497                                                                                                                                                                                                                                                                                                                                                                                                                                    
protein localization to pre-autophagosomal structure                                                                                                                                                                                                                                                                                                                                                                                          
Any process in which a protein is transported to, or maintained at, the pre-autophagosomal structure (PAS).                                                                                                                                                                                                                                                                                                                                   
	
70518
GO:0051292                                                                                                                                                                                                                                                                                                                                                                                                                                    
nuclear pore complex assembly                                                                                                                                                                                                                                                                                                                                                                                                                 
The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.                                                                                                                                                                                                                                                                                                                                      



	
$`6`
		

go_id
Term
Definition

	
778
GO:0000266                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
mitochondrial fission                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
	
834
GO:0000288                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
	
1112
GO:0000413                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
protein peptidyl-prolyl isomerization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The modification of a protein by cis-trans isomerization of a proline residue.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
1904
GO:0001300                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
chronological cell aging                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
	
8906
GO:0006915                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
apoptotic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	
15334
GO:0006337                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
nucleosome disassembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
	
27729
GO:0016559                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
peroxisome fission                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
	
35928
GO:0031055                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
chromatin remodeling at centromere                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Dynamic structural changes in centromeric DNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
40931
GO:0033262                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
regulation of nuclear cell cycle DNA replication                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Any process that modulates the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
	
44172
GO:0034629                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
cellular protein complex localization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
	
50924
GO:0043044                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
ATP-dependent chromatin remodeling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.                                                                                                                                                                                                                                                                                                                                                                                    
	
71694
GO:0051654                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
establishment of mitochondrion localization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The directed movement of the mitochondrion to a specific location.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         



	
$`7`
		

go_id
Term
Definition

	
1129
GO:0000422                                                                                                                                                                                                                                                                                                                                                                                                  
mitophagy                                                                                                                                                                                                                                                                                                                                                                                                   
The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.                                                                                                                                                                                                                                                                         
	
14720
GO:0006081                                                                                                                                                                                                                                                                                                                                                                                                  
cellular aldehyde metabolic process                                                                                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.                                                                                                                                                                                                                                                                  
	
15543
GO:0006470                                                                                                                                                                                                                                                                                                                                                                                                  
protein dephosphorylation                                                                                                                                                                                                                                                                                                                                                                                   
The process of removing one or more phosphoric residues from a protein.                                                                                                                                                                                                                                                                                                                                     
	
16942
GO:0007049                                                                                                                                                                                                                                                                                                                                                                                                  
cell cycle                                                                                                                                                                                                                                                                                                                                                                                                  
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	
60495
GO:0046854                                                                                                                                                                                                                                                                                                                                                                                                  
phosphatidylinositol phosphorylation                                                                                                                                                                                                                                                                                                                                                                        
The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.                                                                                                                                                                                                          
	
64689
GO:0048015                                                                                                                                                                                                                                                                                                                                                                                                  
phosphatidylinositol-mediated signaling                                                                                                                                                                                                                                                                                                                                                                     
A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.                                                                                                                                                                           
	
81920
GO:0072462                                                                                                                                                                                                                                                                                                                                                                                                  
signal transduction involved in meiotic recombination checkpoint                                                                                                                                                                                                                                                                                                                                            
A signal transduction process that contributes to a meiotic recombination checkpoint.                                                                                                                                                                                                                                                                                                                       
	
83833
GO:0090372                                                                                                                                                                                                                                                                                                                                                                                                  
positive regulation of glycerol transport                                                                                                                                                                                                                                                                                                                                                                   
Any process that increases the rate, frequency, or extent of the directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                       
	
105273
GO:1902660                                                                                                                                                                                                                                                                                                                                                                                                  
negative regulation of glucose mediated signaling pathway                                                                                                                                                                                                                                                                                                                                                   
Any process that stops, prevents or reduces the frequency, rate or extent of glucose mediated signaling pathway.                                                                                                                                                                                                                                                                                            
	
131280
GO:2000002                                                                                                                                                                                                                                                                                                                                                                                                  
negative regulation of DNA damage checkpoint                                                                                                                                                                                                                                                                                                                                                                
Any process that stops, prevents, or reduces the frequency, rate or extent of a DNA damage checkpoint.                                                                                                                                                                                                                                                                                                      
	
133408
GO:2001034                                                                                                                                                                                                                                                                                                                                                                                                  
positive regulation of double-strand break repair via nonhomologous end joining                                                                                                                                                                                                                                                                                                                             
Any process that activates or increases the frequency, rate or extent of double-strand break repair via nonhomologous end joining.                                                                                                                                                                                                                                                                          



	
$`8`
		

go_id
Term
Definition

	
48
GO:0000023                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
maltose metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch.                                                                                                                                                                                                                                                                                                                                                                        
	
1282
GO:0000722                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
telomere maintenance via recombination                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
Any recombinational process that contributes to the maintenance of proper telomeric length.                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
1296
GO:0000730                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
DNA recombinase assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.                                                                                                                                                                                                                                                                                                                                                                                                      
	
14466
GO:0005995                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
melibiose catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways resulting in the breakdown of melibiose, the disaccharide 6-O-alpha-D-galactopyranosyl-D-glucose.                                                                                                                                                                                                                                                                                                                                                                                                                 
	
15349
GO:0006348                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
chromatin silencing at telomere                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Repression of transcription of telomeric DNA by altering the structure of chromatin.                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
15756
GO:0006556                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
S-adenosylmethionine biosynthetic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.                                                                                                                                                                                                                                                                                                                                                                             
	
27801
GO:0016584                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nucleosome positioning                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another.                                                                                                                                                                                                                                                                                                                                                                                                                  
	
38010
GO:0032079                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of endodeoxyribonuclease activity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
Any process that activates or increases the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.                                                                                                                                                                                                                                                                                                                                                   
	
43434
GO:0034213                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
quinolinate catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways resulting in the breakdown of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.                                                                                                                                                                                                                                                                                                                                                                                             
	
43723
GO:0034354                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
'de novo' NAD biosynthetic process from tryptophan                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.                                                                                                                                                                                                                                                                                       
	
50306
GO:0042766                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nucleosome mobilization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
The movement of nucleosomes along a DNA fragment.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
	
50814
GO:0043007                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
maintenance of rDNA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any process involved in sustaining the fidelity and copy number of rDNA repeats.                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
	
54302
GO:0070987                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
error-free translesion synthesis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
	
72644
GO:0051983                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
regulation of chromosome segregation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.                                                                                                                                                                                                                                                                                                                
	
131340
GO:2000042                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
negative regulation of double-strand break repair via homologous recombination                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process that stops, prevents, or reduces the frequency, rate or extent of double-strand break repair via homologous recombination.                                                                                                                                                                                                                                                                                                                                                                                                                



	
$`9`
		

go_id
Term
Definition

	
313
GO:0000122                                                                                                                                                                                                                                                                            
negative regulation of transcription from RNA polymerase II promoter                                                                                                                                                                                                                  
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                                                                                                                       
	
845
GO:0000290                                                                                                                                                                                                                                                                            
deadenylation-dependent decapping of nuclear-transcribed mRNA                                                                                                                                                                                                                         
Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.                                                                                                                                                            
	
1176
GO:0000453                                                                                                                                                                                                                                                                            
enzyme-directed rRNA 2'-O-methylation                                                                                                                                                                                                                                                 
The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA.                                                                   
	
12799
GO:0016055                                                                                                                                                                                                                                                                            
Wnt signaling pathway                                                                                                                                                                                                                                                                 
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.                                                                                                         
	
18733
GO:0008360                                                                                                                                                                                                                                                                            
regulation of cell shape                                                                                                                                                                                                                                                              
Any process that modulates the surface configuration of a cell.                                                                                                                                                                                                                       
	
22862
GO:0009749                                                                                                                                                                                                                                                                            
response to glucose                                                                                                                                                                                                                                                                   
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.                                                                                     
	
27304
GO:0016226                                                                                                                                                                                                                                                                            
iron-sulfur cluster assembly                                                                                                                                                                                                                                                          
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.                                                                                                                                                                                                         
	
28775
GO:0017148                                                                                                                                                                                                                                                                            
negative regulation of translation                                                                                                                                                                                                                                                    
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.                                                                                                  
	
28994
GO:0018105                                                                                                                                                                                                                                                                            
peptidyl-serine phosphorylation                                                                                                                                                                                                                                                       
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.                                                                                                                                                                                                           
	
55791
GO:0045429                                                                                                                                                                                                                                                                            
positive regulation of nitric oxide biosynthetic process                                                                                                                                                                                                                              
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.                                                                                                                              
	
75555
GO:0060196                                                                                                                                                                                                                                                                            
positive regulation of antisense RNA transcription                                                                                                                                                                                                                                    
Any process that increases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
	
76504
GO:0060963                                                                                                                                                                                                                                                                            
positive regulation of ribosomal protein gene transcription from RNA polymerase II promoter                                                                                                                                                                                           
Any process that increases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter.                                                                                                     
	
81685
GO:0072363                                                                                                                                                                                                                                                                            
regulation of glycolytic process by positive regulation of transcription from RNA polymerase II promoter                                                                                                                                                                              
Any process that modulates the frequency, rate or extent of glycolysis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                                                                 
	
96687
GO:1901300                                                                                                                                                                                                                                                                            
positive regulation of hydrogen peroxide-mediated programmed cell death                                                                                                                                                                                                               
Any process that activates or increases the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.                                                                                                                                                            



	
$`10`
		

go_id
Term
Definition

	
131
GO:0000050                                                                                                                                                                                                                                                                                                                         
urea cycle                                                                                                                                                                                                                                                                                                                         
The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.                                                                
	
137
GO:0000053                                                                                                                                                                                                                                                                                                                         
argininosuccinate metabolic process                                                                                                                                                                                                                                                                                                
The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate.                                                                                                                               
	
1646
GO:0001015                                                                                                                                                                                                                                                                                                                         
snoRNA transcription from an RNA polymerase II promoter                                                                                                                                                                                                                                                                            
The synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.                                                                                                                                                                                              
	
14756
GO:0006097                                                                                                                                                                                                                                                                                                                         
glyoxylate cycle                                                                                                                                                                                                                                                                                                                   
A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.                                                                                                                                 
	
14802
GO:0055114                                                                                                                                                                                                                                                                                                                         
oxidation-reduction process                                                                                                                                                                                                                                                                                                        
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.                                                                                                                                           
	
15130
GO:0006226                                                                                                                                                                                                                                                                                                                         
dUMP biosynthetic process                                                                                                                                                                                                                                                                                                          
The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).                                                                                                                                                                                                 
	
15660
GO:0006526                                                                                                                                                                                                                                                                                                                         
arginine biosynthetic process                                                                                                                                                                                                                                                                                                      
The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.                                                                                                                                                                                                             
	
21549
GO:0009116                                                                                                                                                                                                                                                                                                                         
nucleoside metabolic process                                                                                                                                                                                                                                                                                                       
The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	
21843
GO:0009229                                                                                                                                                                                                                                                                                                                         
thiamine diphosphate biosynthetic process                                                                                                                                                                                                                                                                                          
The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.                                                                                                                          
	
30269
GO:0018890                                                                                                                                                                                                                                                                                                                         
cyanamide metabolic process                                                                                                                                                                                                                                                                                                        
The chemical reactions and pathways involving cyanamide, NCNH2, a cyanide compound which has been used as a fertilizer, defoliant and in many manufacturing processes. It often occurs as the calcium salt, sometimes also referred to as cyanamide. The citrated calcium salt is used in the treatment of alcoholism.             
	
31229
GO:0019318                                                                                                                                                                                                                                                                                                                         
hexose metabolic process                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.                                                                                                                                                                                                       
	
31298
GO:0019344                                                                                                                                                                                                                                                                                                                         
cysteine biosynthetic process                                                                                                                                                                                                                                                                                                      
The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.                                                                                                                                                                                                                      
	
31819
GO:0019547                                                                                                                                                                                                                                                                                                                         
arginine catabolic process to ornithine                                                                                                                                                                                                                                                                                            
The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.                                                                                                                                                                                                              
	
32472
GO:0019858                                                                                                                                                                                                                                                                                                                         
cytosine metabolic process                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.                                                                                                                  
	
34784
GO:0030643                                                                                                                                                                                                                                                                                                                         
cellular phosphate ion homeostasis                                                                                                                                                                                                                                                                                                 
Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.                                                                                                                                                                                                                      
	
38302
GO:0032211                                                                                                                                                                                                                                                                                                                         
negative regulation of telomere maintenance via telomerase                                                                                                                                                                                                                                                                         
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase.                                                                                                                                                                                                     
	
38435
GO:0032265                                                                                                                                                                                                                                                                                                                         
XMP salvage                                                                                                                                                                                                                                                                                                                        
Any process which produces xanthosine monophosphate from derivatives of it, without de novo synthesis.                                                                                                                                                                                                                             
	
40829
GO:0033194                                                                                                                                                                                                                                                                                                                         
response to hydroperoxide                                                                                                                                                                                                                                                                                                          
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.                                                   
	
46093
GO:0035863                                                                                                                                                                                                                                                                                                                         
dITP catabolic process                                                                                                                                                                                                                                                                                                             
The chemical reactions and pathways resulting in the breakdown of dITP, a deoxyinosine phosphate compound having a triphosphate group at the 5'-position.                                                                                                                                                                          
	
49044
GO:0042262                                                                                                                                                                                                                                                                                                                         
DNA protection                                                                                                                                                                                                                                                                                                                     
Any process in which DNA is protected from damage by, for example, oxidative stress.                                                                                                                                                                                                                                               
	
53373
GO:0044206                                                                                                                                                                                                                                                                                                                         
UMP salvage                                                                                                                                                                                                                                                                                                                        
Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.                                                                                                                                                                                        
	
58376
GO:0046081                                                                                                                                                                                                                                                                                                                         
dUTP catabolic process                                                                                                                                                                                                                                                                                                             
The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.                                                                                                                                                                                                                            
	
58393
GO:0046087                                                                                                                                                                                                                                                                                                                         
cytidine metabolic process                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside.                                                                                                                                                                                                                        
	
58427
GO:0046100                                                                                                                                                                                                                                                                                                                         
hypoxanthine metabolic process                                                                                                                                                                                                                                                                                                     
The chemical reactions and pathways involving hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate.                                                                                                                         
	
59503
GO:0046475                                                                                                                                                                                                                                                                                                                         
glycerophospholipid catabolic process                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways resulting in the breakdown of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.                                                                                                        
	
60470
GO:0046838                                                                                                                                                                                                                                                                                                                         
phosphorylated carbohydrate dephosphorylation                                                                                                                                                                                                                                                                                      
The process of removing a phosphate group from a phosphorylated carbohydrate, any organic compound based on the general formula Cx(H2O)y with a phosphate group attached to it.                                                                                                                                                    
	
76636
GO:0061077                                                                                                                                                                                                                                                                                                                         
chaperone-mediated protein folding                                                                                                                                                                                                                                                                                                 
The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.                                                                                         
	
83829
GO:0090368                                                                                                                                                                                                                                                                                                                         
regulation of ornithine metabolic process                                                                                                                                                                                                                                                                                          
Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.                                  



	
$`11`
		

go_id
Term
Definition

	
199
GO:0000077                                                                                                                                                                                                                         
DNA damage checkpoint                                                                                                                                                                                                              
A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
	
6237
GO:0051017                                                                                                                                                                                                                         
actin filament bundle assembly                                                                                                                                                                                                     
The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.                                        
	
14408
GO:0005978                                                                                                                                                                                                                         
glycogen biosynthetic process                                                                                                                                                                                                      
The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.                                                                       
	
15452
GO:0006406                                                                                                                                                                                                                         
mRNA export from nucleus                                                                                                                                                                                                           
The directed movement of mRNA from the nucleus to the cytoplasm.                                                                                                                                                                   
	
65527
GO:0048478                                                                                                                                                                                                                         
replication fork protection                                                                                                                                                                                                        
Any process that prevents the collapse of stalled replication forks.                                                                                                                                                               
	
71722
GO:0051666                                                                                                                                                                                                                         
actin cortical patch localization                                                                                                                                                                                                  
Any process in which actin cortical patches are transported to, or maintained in, a specific location. An actin cortical patch is a discrete actin-containing structure found just beneath the plasma membrane in fungal cells.    
	
86549
GO:1900027                                                                                                                                                                                                                         
regulation of ruffle assembly                                                                                                                                                                                                      
Any process that modulates the frequency, rate or extent of ruffle assembly.                                                                                                                                                       



	
$`12`
		

go_id
Term
Definition

	
459
GO:0000184                                                                                                                                                                                                                                                                                                                                                                         
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay                                                                                                                                                                                                                                                                                                                
The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.                                                                                                                                      
	
845
GO:0000290                                                                                                                                                                                                                                                                                                                                                                         
deadenylation-dependent decapping of nuclear-transcribed mRNA                                                                                                                                                                                                                                                                                                                      
Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.                                                                                                                                                                                                                                                         
	
1325
GO:0000742                                                                                                                                                                                                                                                                                                                                                                         
karyogamy involved in conjugation with cellular fusion                                                                                                                                                                                                                                                                                                                             
During sexual reproduction, the creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. This occurs after cytogamy.                                                                                                                                                                                                  
	
1908
GO:0001302                                                                                                                                                                                                                                                                                                                                                                         
replicative cell aging                                                                                                                                                                                                                                                                                                                                                             
The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.                                                                                                                                                                                                                 
	
2003
GO:0001403                                                                                                                                                                                                                                                                                                                                                                         
invasive growth in response to glucose limitation                                                                                                                                                                                                                                                                                                                                  
A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
	
6214
GO:0006986                                                                                                                                                                                                                                                                                                                                                                         
response to unfolded protein                                                                                                                                                                                                                                                                                                                                                       
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.                                                                                                                                                                        
	
9653
GO:0007155                                                                                                                                                                                                                                                                                                                                                                         
cell adhesion                                                                                                                                                                                                                                                                                                                                                                      
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.                                                                                                                                                                                                                                      
	
15257
GO:0006279                                                                                                                                                                                                                                                                                                                                                                         
premeiotic DNA replication                                                                                                                                                                                                                                                                                                                                                         
The replication of DNA that precedes meiotic cell division.                                                                                                                                                                                                                                                                                                                        
	
15538
GO:0006468                                                                                                                                                                                                                                                                                                                                                                         
protein phosphorylation                                                                                                                                                                                                                                                                                                                                                            
The process of introducing a phosphate group on to a protein.                                                                                                                                                                                                                                                                                                                      
	
16856
GO:0006995                                                                                                                                                                                                                                                                                                                                                                         
cellular response to nitrogen starvation                                                                                                                                                                                                                                                                                                                                           
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.                                                                                                                                                                                            
	
17061
GO:0007126                                                                                                                                                                                                                                                                                                                                                                         
meiotic nuclear division                                                                                                                                                                                                                                                                                                                                                           
One of the two nuclear divisions that occur as part of the meiotic cell cycle.                                                                                                                                                                                                                                                                                                     
	
17480
GO:0007329                                                                                                                                                                                                                                                                                                                                                                         
positive regulation of transcription from RNA polymerase II promoter by pheromones                                                                                                                                                                                                                                                                                                 
Any process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter.                                                                                                                                                                                                                                                         
	
26891
GO:0045722                                                                                                                                                                                                                                                                                                                                                                         
positive regulation of gluconeogenesis                                                                                                                                                                                                                                                                                                                                             
Any process that activates or increases the frequency, rate or extent of gluconeogenesis.                                                                                                                                                                                                                                                                                          
	
27320
GO:0016239                                                                                                                                                                                                                                                                                                                                                                         
positive regulation of macroautophagy                                                                                                                                                                                                                                                                                                                                              
Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.                                                                                                                                                                                          
	
28775
GO:0017148                                                                                                                                                                                                                                                                                                                                                                         
negative regulation of translation                                                                                                                                                                                                                                                                                                                                                 
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.                                                                                                                                                                                               
	
34445
GO:0030435                                                                                                                                                                                                                                                                                                                                                                         
sporulation resulting in formation of a cellular spore                                                                                                                                                                                                                                                                                                                             
The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.                                                                                                            
	
36000
GO:0031087                                                                                                                                                                                                                                                                                                                                                                         
deadenylation-independent decapping of nuclear-transcribed mRNA                                                                                                                                                                                                                                                                                                                    
Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.                                                                                                                                                                                                                                                                               
	
58248
GO:0046020                                                                                                                                                                                                                                                                                                                                                                         
negative regulation of transcription from RNA polymerase II promoter by pheromones                                                                                                                                                                                                                                                                                                 
Any process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.                                                                                                                                                                                                                                                     
	
82920
GO:0080009                                                                                                                                                                                                                                                                                                                                                                         
mRNA methylation                                                                                                                                                                                                                                                                                                                                                                   
The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.                                                                                                                                                                                                                                                                                        
	
84089
GO:0090606                                                                                                                                                                                                                                                                                                                                                                         
single-species surface biofilm formation                                                                                                                                                                                                                                                                                                                                           
A process in which planktonically growing microorganisms of the same species grow at the surface of a liquid-air interface and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.                                                                                                        
	
90262
GO:1900436                                                                                                                                                                                                                                                                                                                                                                         
positive regulation of filamentous growth of a population of unicellular organisms in response to starvation                                                                                                                                                                                                                                                                       
Any process that activates or increases the frequency, rate or extent of filamentous growth of a population of unicellular organisms in response to starvation.                                                                                                                                                                                                                    
	
131765
GO:2000221                                                                                                                                                                                                                                                                                                                                                                         
negative regulation of pseudohyphal growth                                                                                                                                                                                                                                                                                                                                         
Any process that stops, prevents, or reduces the frequency, rate or extent of pseudohyphal growth.                                                                                                                                                                                                                                                                                 



	
$`13`
		

go_id
Term
Definition

	
459
GO:0000184                                                                                                                                                                                                                                   
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay                                                                                                                                                                          
The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	
845
GO:0000290                                                                                                                                                                                                                                   
deadenylation-dependent decapping of nuclear-transcribed mRNA                                                                                                                                                                                
Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.                                                                                                                   
	
15431
GO:0006397                                                                                                                                                                                                                                   
mRNA processing                                                                                                                                                                                                                              
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.                                                                                                   
	
24222
GO:0010501                                                                                                                                                                                                                                   
RNA secondary structure unwinding                                                                                                                                                                                                            
The process in which a secondary structure of RNA are broken or 'melted'.                                                                                                                                                                    
	
36000
GO:0031087                                                                                                                                                                                                                                   
deadenylation-independent decapping of nuclear-transcribed mRNA                                                                                                                                                                              
Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.                                                                                                                                         
	
42789
GO:0033962                                                                                                                                                                                                                                   
cytoplasmic mRNA processing body assembly                                                                                                                                                                                                    
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.                                                                                                                  
	
43172
GO:0034063                                                                                                                                                                                                                                   
stress granule assembly                                                                                                                                                                                                                      
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.                                                                                                                                    
	
57664
GO:0045900                                                                                                                                                                                                                                   
negative regulation of translational elongation                                                                                                                                                                                              
Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.                                                                                                                                      
	
69682
GO:0051028                                                                                                                                                                                                                                   
mRNA transport                                                                                                                                                                                                                               
The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                            
	
75645
GO:0060261                                                                                                                                                                                                                                   
positive regulation of transcription initiation from RNA polymerase II promoter                                                                                                                                                              
Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.                                                                                                 
	
87636
GO:1900153                                                                                                                                                                                                                                   
positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                             
Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.                                                                                          



	
$`14`
		

go_id
Term
Definition

	
131
GO:0000050                                                                                                                                                                                                                                                                                                                               
urea cycle                                                                                                                                                                                                                                                                                                                               
The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.                                                                      
	
1293
GO:0000727                                                                                                                                                                                                                                                                                                                               
double-strand break repair via break-induced replication                                                                                                                                                                                                                                                                                 
The error-free repair of a double-strand break in DNA in which the centromere-proximal end of a broken chromosome searches for a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template, and progresses to the end of the chromosome.
	
1737
GO:0001100                                                                                                                                                                                                                                                                                                                               
negative regulation of exit from mitosis                                                                                                                                                                                                                                                                                                 
Any process involved in the inhibition of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).                                                                                                                                                                                              
	
15257
GO:0006279                                                                                                                                                                                                                                                                                                                               
premeiotic DNA replication                                                                                                                                                                                                                                                                                                               
The replication of DNA that precedes meiotic cell division.                                                                                                                                                                                                                                                                              
	
16705
GO:0006909                                                                                                                                                                                                                                                                                                                               
phagocytosis                                                                                                                                                                                                                                                                                                                             
An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.                                                                        
	
16875
GO:0007004                                                                                                                                                                                                                                                                                                                               
telomere maintenance via telomerase                                                                                                                                                                                                                                                                                                      
The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.                                                                                                                                                                                                                                           
	
18733
GO:0008360                                                                                                                                                                                                                                                                                                                               
regulation of cell shape                                                                                                                                                                                                                                                                                                                 
Any process that modulates the surface configuration of a cell.                                                                                                                                                                                                                                                                          
	
28994
GO:0018105                                                                                                                                                                                                                                                                                                                               
peptidyl-serine phosphorylation                                                                                                                                                                                                                                                                                                          
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.                                                                                                                                                                                                                                                              
	
37687
GO:0031938                                                                                                                                                                                                                                                                                                                               
regulation of chromatin silencing at telomere                                                                                                                                                                                                                                                                                            
Any process that affects the rate, extent or location of chromatin silencing at telomeres.                                                                                                                                                                                                                                               
	
49610
GO:0042450                                                                                                                                                                                                                                                                                                                               
arginine biosynthetic process via ornithine                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.                                                                                                                                                                                  
	
55054
GO:0045332                                                                                                                                                                                                                                                                                                                               
phospholipid translocation                                                                                                                                                                                                                                                                                                               
The movement of a phospholipid molecule from one leaflet of a membrane bilayer to the opposite leaflet.                                                                                                                                                                                                                                  
	
111245
GO:1903343                                                                                                                                                                                                                                                                                                                               
positive regulation of meiotic DNA double-strand break formation                                                                                                                                                                                                                                                                         
Any process that activates or increases the frequency, rate or extent of meiotic DNA double-strand break formation.                                                                                                                                                                                                                      



	
$`15`
		

go_id
Term
Definition

	
47807
GO:0038203                                                                                                                                                                                                                          
TORC2 signaling                                                                                                                                                                                                                     
A series of intracellular molecular signals mediated by TORC2; TOR (rapamycin-insensitive companion of TOR) in complex with at least Rictor (regulatory-associated protein of TOR), or orthologs of, and other signaling components.



	
$`16`
		

go_id
Term
Definition

	
459
GO:0000184                                                                                                                                                                                                                                         
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay                                                                                                                                                                                
The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.      
	
15405
GO:0006378                                                                                                                                                                                                                                         
mRNA polyadenylation                                                                                                                                                                                                                               
The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.                                                                                                                            
	
15518
GO:0006446                                                                                                                                                                                                                                         
regulation of translational initiation                                                                                                                                                                                                             
Any process that modulates the frequency, rate or extent of translational initiation.                                                                                                                                                              
	
28410
GO:0016973                                                                                                                                                                                                                                         
poly(A)+ mRNA export from nucleus                                                                                                                                                                                                                  
The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.                                                                                                                                                                      
	
31714
GO:0019509                                                                                                                                                                                                                                         
L-methionine biosynthetic process from methylthioadenosine                                                                                                                                                                                         
The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.                                                                                                                                                     
	
51986
GO:0043488                                                                                                                                                                                                                                         
regulation of mRNA stability                                                                                                                                                                                                                       
Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.                                                                                                          
	
57884
GO:0045945                                                                                                                                                                                                                                         
positive regulation of transcription from RNA polymerase III promoter                                                                                                                                                                              
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter.                                                                                                                        
	
81832
GO:0072423                                                                                                                                                                                                                                         
response to DNA damage checkpoint signaling                                                                                                                                                                                                        
A process that occurs in response to signals generated as a result of DNA damage checkpoint signaling.                                                                                                                                             
	
85632
GO:0098789                                                                                                                                                                                                                                         
pre-mRNA cleavage required for polyadenylation                                                                                                                                                                                                     
The targeted, endonucleolytic cleavage of a pre-mRNA,  required for polyadenylation of the 3' end.  This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
	
87592
GO:1900152                                                                                                                                                                                                                                         
negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                                   
Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.                                                                                            
	
89630
GO:1900364                                                                                                                                                                                                                                         
negative regulation of mRNA polyadenylation                                                                                                                                                                                                        
Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.                                                                                                                                                 
	
115186
GO:1903833                                                                                                                                                                                                                                         
positive regulation of cellular response to amino acid starvation                                                                                                                                                                                  
Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.                                                                                                                               



	
$`17`
		

go_id
Term
Definition

	
7108
GO:0006606                                                                                                                                                                                                                                                                                                            
protein import into nucleus                                                                                                                                                                                                                                                                                           
The directed movement of a protein from the cytoplasm to the nucleus.                                                                                                                                                                                                                                                 
	
15892
GO:0006607                                                                                                                                                                                                                                                                                                            
NLS-bearing protein import into nucleus                                                                                                                                                                                                                                                                               
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.                                                                                                                                                                      
	
16709
GO:0006913                                                                                                                                                                                                                                                                                                            
nucleocytoplasmic transport                                                                                                                                                                                                                                                                                           
The directed movement of molecules between the nucleus and the cytoplasm.                                                                                                                                                                                                                                             
	
16867
GO:0006999                                                                                                                                                                                                                                                                                                            
nuclear pore organization                                                                                                                                                                                                                                                                                             
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.                                                                                                                                                              
	
25377
GO:0015031                                                                                                                                                                                                                                                                                                            
protein transport                                                                                                                                                                                                                                                                                                     
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                              
	
34486
GO:0030474                                                                                                                                                                                                                                                                                                            
spindle pole body duplication                                                                                                                                                                                                                                                                                         
Construction of a new spindle pole body.                                                                                                                                                                                                                                                                              
	
37784
GO:0031990                                                                                                                                                                                                                                                                                                            
mRNA export from nucleus in response to heat stress                                                                                                                                                                                                                                                                   
The directed movement of mRNA from the nucleus to the cytoplasm during a heat stimulus, a temperature stimulus above the optimal temperature for the organism; in particular, a process that enables an organism withstand exposure to temperatures that would otherwise lethally impair poly(A)+ mRNA-nucleus export.
	
44020
GO:0034501                                                                                                                                                                                                                                                                                                            
protein localization to kinetochore                                                                                                                                                                                                                                                                                   
Any process in which a protein is transported to, or maintained at, the kinetochore.                                                                                                                                                                                                                                  
	
69682
GO:0051028                                                                                                                                                                                                                                                                                                            
mRNA transport                                                                                                                                                                                                                                                                                                        
The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                     
	
70542
GO:0051301                                                                                                                                                                                                                                                                                                            
cell division                                                                                                                                                                                                                                                                                                         
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                                        
	
75547
GO:0060188                                                                                                                                                                                                                                                                                                            
regulation of protein desumoylation                                                                                                                                                                                                                                                                                   
Any process that modulates the frequency, rate or extent of protein desumoylation. Protein desumoylation is the process in which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.                                                                                                
	
81826
GO:0072417                                                                                                                                                                                                                                                                                                            
response to spindle checkpoint signaling                                                                                                                                                                                                                                                                              
A process that occurs in response to signals generated as a result of spindle checkpoint signaling.                                                                                                                                                                                                                   



	
$`18`
		

go_id
Term
Definition

	
97
GO:0000045                                                                                                                                                                                                                                                                                                     
autophagosome assembly                                                                                                                                                                                                                                                                                         
The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.                                                                                                             
	
1129
GO:0000422                                                                                                                                                                                                                                                                                                     
mitophagy                                                                                                                                                                                                                                                                                                      
The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.                                                                                                                                                                            
	
16856
GO:0006995                                                                                                                                                                                                                                                                                                     
cellular response to nitrogen starvation                                                                                                                                                                                                                                                                       
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.                                                                                                                        
	
24220
GO:0010499                                                                                                                                                                                                                                                                                                     
proteasomal ubiquitin-independent protein catabolic process                                                                                                                                                                                                                                                    
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome but do not involve ubiquitin.                                                                                                                     
	
24223
GO:0010506                                                                                                                                                                                                                                                                                                     
regulation of autophagy                                                                                                                                                                                                                                                                                        
Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.                                                                                                                                                            
	
38193
GO:0032147                                                                                                                                                                                                                                                                                                     
activation of protein kinase activity                                                                                                                                                                                                                                                                          
Any process that initiates the activity of an inactive protein kinase.                                                                                                                                                                                                                                         
	
38427
GO:0032258                                                                                                                                                                                                                                                                                                     
CVT pathway                                                                                                                                                                                                                                                                                                    
A constitutive biosynthetic process that occurs under nutrient-rich conditions, in which two resident vacuolar hydrolases, aminopeptidase I and alpha-mannosidase, are sequestered into vesicles; these vesicles are transported to, and then fuse with, the vacuole. This pathway is mostly observed in yeast.
	
44014
GO:0034497                                                                                                                                                                                                                                                                                                     
protein localization to pre-autophagosomal structure                                                                                                                                                                                                                                                           
Any process in which a protein is transported to, or maintained at, the pre-autophagosomal structure (PAS).                                                                                                                                                                                                    
	
44374
GO:0034727                                                                                                                                                                                                                                                                                                     
piecemeal microautophagy of nucleus                                                                                                                                                                                                                                                                            
Degradation of a cell nucleus by lysosomal microautophagy.                                                                                                                                                                                                                                                     
	
53373
GO:0044206                                                                                                                                                                                                                                                                                                     
UMP salvage                                                                                                                                                                                                                                                                                                    
Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.                                                                                                                                                                    
	
54185
GO:0044805                                                                                                                                                                                                                                                                                                     
late nucleophagy                                                                                                                                                                                                                                                                                               
A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.                                                                                                    
	
60341
GO:0046777                                                                                                                                                                                                                                                                                                     
protein autophosphorylation                                                                                                                                                                                                                                                                                    
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).                                                                                                                                     
	
77340
GO:0061709                                                                                                                                                                                                                                                                                                     
reticulophagy                                                                                                                                                                                                                                                                                                  
The autophagic process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions.                                                                                                                         



	
$`19`
		

go_id
Term
Definition

	
32
GO:0000011                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
vacuole inheritance                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.                                                                                                                                                                                                                                                                                                                                                                                                            
	
989
GO:0000350                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
generation of catalytic spliceosome for second transesterification step                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Conformational rearrangement of the spliceosomal complex containing the RNA products from the 1st step of splicing to form the catalytic site for the second step of splicing.                                                                                                                                                                                                                                                                                                                                                                        
	
1191
GO:0000467                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)                                                                                                                                                                                                                                                                                                                                                                                                                      
Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.                                                                                                                                                                                                                              
	
1248
GO:0000707                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
meiotic DNA recombinase assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
During meiosis, the aggregation, arrangement and bonding together of strand exchange proteins (recombinases) to form higher order oligomers on single-stranded DNA.                                                                                                                                                                                                                                                                                                                                                                                   
	
1296
GO:0000730                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
DNA recombinase assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.                                                                                                                                                                                                                                                                                                                                                                                                      
	
14478
GO:0006000                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
fructose metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.                                                                                                                                                                                                                                                                                              
	
14483
GO:0006003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
fructose 2,6-bisphosphate metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase.                                                                                                                                                                                                                                                                                                          
	
14732
GO:0006086                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
acetyl-CoA biosynthetic process from pyruvate                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
14749
GO:0006096                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
glycolytic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.                                                                                                        
	
14779
GO:0006110                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
regulation of glycolytic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that modulates the frequency, rate or extent of glycolysis.                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
	
16687
GO:0006896                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Golgi to vacuole transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The directed movement of substances from the Golgi to the vacuole.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
	
23814
GO:0010212                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
response to ionizing radiation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.                                                                                          
	
43979
GO:0034473                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
U1 snRNA 3'-end processing                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Any process involved in forming the mature 3' end of a U1 snRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
43981
GO:0034475                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
U4 snRNA 3'-end processing                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Any process involved in forming the mature 3' end of a U4 snRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
43982
GO:0034476                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
U5 snRNA 3'-end processing                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Any process involved in forming the mature 3' end of a U5 snRNA molecule.                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
48683
GO:0042148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
strand invasion                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules.                                                                                                                                                                
	
50814
GO:0043007                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
maintenance of rDNA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any process involved in sustaining the fidelity and copy number of rDNA repeats.                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
	
54302
GO:0070987                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
error-free translesion synthesis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
	
65162
GO:0048278                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
vesicle docking                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The initial attachment of a transport vesicle membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere.                                                                                                                                                                                                                                                                    
	
78514
GO:0070478                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.                                                                                                                                                                                                                                                 
	
78529
GO:0070481                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear-transcribed mRNA catabolic process, non-stop decay                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.                                                                                                                                                                                                                                                                                                                                                                                                     
	
78925
GO:0070651                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nonfunctional rRNA decay                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
An rRNA catabolic process that results in the targeted detection and degradation of aberrant rRNAs contained within translationally defective ribosomes, thereby acting as a quality-control system.                                                                                                                                                                                                                                                                                                                                                  
	
79654
GO:0071028                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear mRNA surveillance                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The set of processes involved in identifying and degrading defective or aberrant mRNAs within the nucleus.                                                                                                                                                                                                                                                                                                                                                                                                                                            
	
79666
GO:0071035                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear polyadenylation-dependent rRNA catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA.                                                                                                                                                                              
	
79669
GO:0071038                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear polyadenylation-dependent tRNA catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of an aberrant or incorrectly modified transfer RNA (tRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target tRNA.                                                                                                                                                                                                                                                              
	
79670
GO:0071039                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear polyadenylation-dependent CUT catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a cryptic unstable transcript (CUT), initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target CUT.                                                                                                                                                                                                                                                                                            
	
79673
GO:0071042                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
nuclear polyadenylation-dependent mRNA catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a messenger RNA (mRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target mRNA.                                                                                                                                                                                                                                                                                               
	
79682
GO:0071051                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
polyadenylation-dependent snoRNA 3'-end processing                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Any process involved in forming the mature 3' end of a snoRNA molecule linked to prior polyadenylation of the 3'-end of the precursor snoRNA.                                                                                                                                                                                                                                                                                                                                                                                                         



	
$`20`
		

go_id
Term
Definition

	
143
GO:0000055                                                                                                                                                       
ribosomal large subunit export from nucleus                                                                                                                      
The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.                                                                          
	
150
GO:0000056                                                                                                                                                       
ribosomal small subunit export from nucleus                                                                                                                      
The directed movement of a ribosomal small subunit from the nucleus into the cytoplasm.                                                                          
	
7108
GO:0006606                                                                                                                                                       
protein import into nucleus                                                                                                                                      
The directed movement of a protein from the cytoplasm to the nucleus.                                                                                            
	
15464
GO:0006409                                                                                                                                                       
tRNA export from nucleus                                                                                                                                         
The directed movement of tRNA from the nucleus to the cytoplasm.                                                                                                 
	
15892
GO:0006607                                                                                                                                                       
NLS-bearing protein import into nucleus                                                                                                                          
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.                 
	
16867
GO:0006999                                                                                                                                                       
nuclear pore organization                                                                                                                                        
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.         
	
28410
GO:0016973                                                                                                                                                       
poly(A)+ mRNA export from nucleus                                                                                                                                
The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.                                                                                    
	
46845
GO:0036228                                                                                                                                                       
protein targeting to nuclear inner membrane                                                                                                                      
The process of targeting a protein to, and inserting it into, the nuclear inner membrane; usually uses signals contained within the protein.                     
	
69682
GO:0051028                                                                                                                                                       
mRNA transport                                                                                                                                                   
The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	
84320
GO:0097064                                                                                                                                                       
ncRNA export from nucleus                                                                                                                                        
The directed movement of a non-coding RNA transcript (ncRNA) from the nucleus to the cytoplasm.                                                                  



	
$`21`
		

go_id
Term
Definition

	
27785
GO:0016573                                                                                                                                                                                                                               
histone acetylation                                                                                                                                                                                                                      
The modification of a histone by the addition of an acetyl group.                                                                                                                                                                        
	
69841
GO:0051090                                                                                                                                                                                                                               
regulation of sequence-specific DNA binding transcription factor activity                                                                                                                                                                
Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.                                                                
	
69919
GO:0051123                                                                                                                                                                                                                               
RNA polymerase II transcriptional preinitiation complex assembly                                                                                                                                                                         
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.



	
$`22`
		

go_id
Term
Definition

	
1283
GO:0000723                                                                                                                                                                                                                                                                                                                              
telomere maintenance                                                                                                                                                                                                                                                                                                                    
Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
	
15349
GO:0006348                                                                                                                                                                                                                                                                                                                              
chromatin silencing at telomere                                                                                                                                                                                                                                                                                                         
Repression of transcription of telomeric DNA by altering the structure of chromatin.                                                                                                                                                                                                                                                    
	
71434
GO:0051568                                                                                                                                                                                                                                                                                                                              
histone H3-K4 methylation                                                                                                                                                                                                                                                                                                               
The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.                                                                                                                                                                                                                         
	
83140
GO:0080182                                                                                                                                                                                                                                                                                                                              
histone H3-K4 trimethylation                                                                                                                                                                                                                                                                                                            
The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.                                                                                                                                                                                                                               



	
$`23`
		

go_id
Term
Definition

	
14802
GO:0055114                                                                                                                                                                              
oxidation-reduction process                                                                                                                                                             
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	
21362
GO:0009060                                                                                                                                                                              
aerobic respiration                                                                                                                                                                     
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.                       
	
31828
GO:0019551                                                                                                                                                                              
glutamate catabolic process to 2-oxoglutarate                                                                                                                                           
The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including 2-oxoglutarate.                                                             



	
$`24`
		

go_id
Term
Definition

	
203
GO:0000079                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
regulation of cyclin-dependent protein serine/threonine kinase activity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
	
207
GO:0000083                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
regulation of transcription involved in G1/S transition of mitotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
	
1304
GO:0000733                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
DNA strand renaturation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The identification and annealing of complementary base pairs in single-strand DNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
	
15268
GO:0006282                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
regulation of DNA repair                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that modulates the frequency, rate or extent of DNA repair.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
	
17027
GO:0007094                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
mitotic spindle assembly checkpoint                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.                                                                                                                                                                                                                                                                                                                                                                                                                                     
	
18735
GO:0008361                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
regulation of cell size                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that modulates the size of a cell.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
	
36107
GO:0031145                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
anaphase-promoting complex-dependent catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.                                                                                                                                                                                                                                                                                                                                    
	
39960
GO:0032837                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
distributive segregation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during a normally chiasmate meiosis under the condition that chiasma have not occurred between a particular pair of homologs. Distributive segregation is a "backup" mechanism to ensure the segregation of homologs that have failed to cross over - either as a consequence of mutation or not, as, for example, the 4th chromosome of Drosophila melanogaster (which never exchanges, presumably due to its small size) - but nevertheless segregate normally.
	
41617
GO:0033567                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
DNA replication, Okazaki fragment processing                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.                                                                                                                                                                                                                                                                                                                                                                                             
	
48677
GO:0042144                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
vacuole fusion, non-autophagic                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The fusion of two vacuole membranes to form a single vacuole.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
	
54154
GO:0044774                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
mitotic DNA integrity checkpoint                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
A mitotic cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and ends with signal transduction.                                                                                                                                                                                                                                                                                                                           
	
56958
GO:0045732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
positive regulation of protein catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.                                                                                                                                                                                                                                                                                                                                                                 
	
57437
GO:0045842                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
positive regulation of mitotic metaphase/anaphase transition                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Any process that activates or increases the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.                                                                                                                                                                                                                                                                                                                      
	
70542
GO:0051301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
cell division                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                                                                                                                                                                                                                                                                                                                                                
	
70564
GO:0051312                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
chromosome decondensation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The alteration of chromosome structure from the condensed form to a relaxed disperse form.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
	
70937
GO:0051441                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
positive regulation of ubiquitin-protein ligase activity involved in meiotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that activates, maintains or increases the rate of ubiquitin ligase activity during the meiotic cell cycle.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       



	
$`25`
		

go_id
Term
Definition

	
16924
GO:0007032                                                                                                                                          
endosome organization                                                                                                                               
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.   
	
40062
GO:0032880                                                                                                                                          
regulation of protein localization                                                                                                                  
Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.



	
$`26`
		

go_id
Term
Definition

	
15518
GO:0006446                                                                                                                                                             
regulation of translational initiation                                                                                                                                 
Any process that modulates the frequency, rate or extent of translational initiation.                                                                                  
	
16683
GO:0006895                                                                                                                                                             
Golgi to endosome transport                                                                                                                                            
The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes.               
	
26327
GO:0015693                                                                                                                                                             
magnesium ion transport                                                                                                                                                
The directed movement of magnesium (Mg) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                    
	
31714
GO:0019509                                                                                                                                                             
L-methionine biosynthetic process from methylthioadenosine                                                                                                             
The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.                                                                         
	
38972
GO:0032511                                                                                                                                                             
late endosome to vacuole transport via multivesicular body sorting pathway                                                                                             
The directed movement of substances from endosomes to vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the vacuole.
	
46464
GO:0036010                                                                                                                                                             
protein localization to endosome                                                                                                                                       
A process in which a protein is transported to, or maintained in, a location within an endosome.                                                                       
	
85530
GO:0098655                                                                                                                                                             
cation transmembrane transport                                                                                                                                         
A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.                              



	
$`27`
		

go_id
Term
Definition

	
1481
GO:0000902                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
cell morphogenesis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
The developmental process in which the size or shape of a cell is generated and organized.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
	
1530
GO:0000920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
cell separation after cytokinesis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
	
1764
GO:0001113                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
transcriptional open complex formation at RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.                                                                                                                                                                                                                                                                                                                                                                                              
	
15278
GO:0006289                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
nucleotide-excision repair                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).                                                                                                                                                                                                                                                
	
15393
GO:0006367                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
transcription initiation from RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.                                                                                                                                              
	
17053
GO:0007118                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
budding cell apical bud growth                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Growth at the tip of a bud, in a cell that reproduces by budding.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
27479
GO:0042981                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
regulation of apoptotic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Any process that modulates the occurrence or rate of cell death by apoptotic process.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
	
33635
GO:0023014                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
signal transduction by protein phosphorylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
	
36012
GO:0031098                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
stress-activated protein kinase signaling cascade                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
A series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays one or more of the signals.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
	
38193
GO:0032147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
activation of protein kinase activity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process that initiates the activity of an inactive protein kinase.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
79215
GO:0070816                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
phosphorylation of RNA polymerase II C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex.



	
$`28`
		

go_id
Term
Definition

	
1908
GO:0001302                                                                                                                                                                                                                                                                                                                                                                         
replicative cell aging                                                                                                                                                                                                                                                                                                                                                             
The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.                                                                                                                                                                                                                 
	
2003
GO:0001403                                                                                                                                                                                                                                                                                                                                                                         
invasive growth in response to glucose limitation                                                                                                                                                                                                                                                                                                                                  
A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
	
15456
GO:0006407                                                                                                                                                                                                                                                                                                                                                                         
rRNA export from nucleus                                                                                                                                                                                                                                                                                                                                                           
The directed movement of rRNA from the nucleus to the cytoplasm; the rRNA is usually in the form of ribonucleoproteins.                                                                                                                                                                                                                                                            
	
48688
GO:0042149                                                                                                                                                                                                                                                                                                                                                                         
cellular response to glucose starvation                                                                                                                                                                                                                                                                                                                                            
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of glucose.                                                                                                                                                                                             
	
51307
GO:0043254                                                                                                                                                                                                                                                                                                                                                                         
regulation of protein complex assembly                                                                                                                                                                                                                                                                                                                                             
Any process that modulates the frequency, rate or extent of protein complex assembly.                                                                                                                                                                                                                                                                                              
	
87636
GO:1900153                                                                                                                                                                                                                                                                                                                                                                         
positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay                                                                                                                                                                                                                                                                                   
Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.                                                                                                                                                                                                                                



	
$`29`
		

go_id
Term
Definition

	
69
GO:0000032                                                                                                                                                                                                                                                                                            
cell wall mannoprotein biosynthetic process                                                                                                                                                                                                                                                           
The chemical reactions and pathways resulting in the formation of cell wall mannoproteins, any cell wall protein that contains covalently bound mannose residues.                                                                                                                                     
	
335
GO:0000132                                                                                                                                                                                                                                                                                            
establishment of mitotic spindle orientation                                                                                                                                                                                                                                                          
A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.                                                                                                                                                                                                
	
1282
GO:0000722                                                                                                                                                                                                                                                                                            
telomere maintenance via recombination                                                                                                                                                                                                                                                                
Any recombinational process that contributes to the maintenance of proper telomeric length.                                                                                                                                                                                                           
	
16897
GO:0007020                                                                                                                                                                                                                                                                                            
microtubule nucleation                                                                                                                                                                                                                                                                                
The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).   
	
16950
GO:0007052                                                                                                                                                                                                                                                                                            
mitotic spindle organization                                                                                                                                                                                                                                                                          
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.                                                                                                           
	
16968
GO:0007067                                                                                                                                                                                                                                                                                            
mitotic nuclear division                                                                                                                                                                                                                                                                              
A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
	
17031
GO:0007097                                                                                                                                                                                                                                                                                            
nuclear migration                                                                                                                                                                                                                                                                                     
The directed movement of the nucleus.                                                                                                                                                                                                                                                                 
	
36049
GO:0031116                                                                                                                                                                                                                                                                                            
positive regulation of microtubule polymerization                                                                                                                                                                                                                                                     
Any process that activates or increases the frequency, rate or extent of microtubule polymerization.                                                                                                                                                                                                  
	
37063
GO:0031578                                                                                                                                                                                                                                                                                            
mitotic spindle orientation checkpoint                                                                                                                                                                                                                                                                
A cell cycle checkpoint that monitors and signals errors in the placement or orientation of the spindle in the cell. This delays the completion of anaphase until errors are corrected.                                                                                                               
	
44020
GO:0034501                                                                                                                                                                                                                                                                                            
protein localization to kinetochore                                                                                                                                                                                                                                                                   
Any process in which a protein is transported to, or maintained at, the kinetochore.                                                                                                                                                                                                                  
	
70542
GO:0051301                                                                                                                                                                                                                                                                                            
cell division                                                                                                                                                                                                                                                                                         
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                        
	
70565
GO:0051315                                                                                                                                                                                                                                                                                            
attachment of mitotic spindle microtubules to kinetochore                                                                                                                                                                                                                                             
The cell cycle process in which spindle microtubules become physically associated with the proteins making up the kinetochore complex as part of mitotic metaphase plate congression.                                                                                                                 
	
72658
GO:0051987                                                                                                                                                                                                                                                                                            
positive regulation of attachment of spindle microtubules to kinetochore                                                                                                                                                                                                                              
Any process that activates or increases the frequency, rate or extent of the attachment of spindle microtubules to the kinetochore.                                                                                                                                                                   



	
$`30`
		

go_id
Term
Definition

	
1596
GO:0000972                                                                                                                                                                                                                                                                                                                                                                                            
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery                                                                                                                                                                                                                                                                                                                  
The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
	
40661
GO:0043547                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of GTPase activity                                                                                                                                                                                                                                                                                                                                                                
Any process that activates or increases the activity of a GTPase.                                                                                                                                                                                                                                                                                                                                     
	
78983
GO:0070682                                                                                                                                                                                                                                                                                                                                                                                            
proteasome regulatory particle assembly                                                                                                                                                                                                                                                                                                                                                               
The aggregation, arrangement and bonding together of a mature, active proteasome regulatory particle complex.                                                                                                                                                                                                                                                                                         
	
119613
GO:1904263                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of TORC1 signaling                                                                                                                                                                                                                                                                                                                                                                
Any process that activates or increases the frequency, rate or extent of TORC1 signaling.                                                                                                                                                                                                                                                                                                             
	
133559
GO:2001158                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of proline catabolic process to glutamate                                                                                                                                                                                                                                                                                                                                         
Any process that activates or increases the frequency, rate or extent of proline catabolic process to glutamate.                                                                                                                                                                                                                                                                                      



	
$`31`
		

go_id
Term
Definition

	
979
GO:0000349                                                                                                                                                                                                                                                                                                                                    
generation of catalytic spliceosome for first transesterification step                                                                                                                                                                                                                                                                        
Formation of a catalytic spliceosome complex ready to perform the first splicing reaction. This occurs by an ATP-dependent conformational change of the pre-catalytic spliceosome.                                                                                                                                                            
	
1168
GO:0000447                                                                                                                                                                                                                                                                                                                                    
endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)                                                                                                                                                                                           
Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.                                            
	
1196
GO:0000472                                                                                                                                                                                                                                                                                                                                    
endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)                                                                                                                                                                                                                                           
Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.
	
40318
GO:0032958                                                                                                                                                                                                                                                                                                                                    
inositol phosphate biosynthetic process                                                                                                                                                                                                                                                                                                       
The chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.                                                                                                                                                                            
	
43515
GO:0034247                                                                                                                                                                                                                                                                                                                                    
snoRNA splicing                                                                                                                                                                                                                                                                                                                               
The process of removing sections of a primary snoRNA transcript to remove sequences not present in the mature form of the snoRNA and joining the remaining sections to form the mature form of the snoRNA.                                                                                                                                    
	
78529
GO:0070481                                                                                                                                                                                                                                                                                                                                    
nuclear-transcribed mRNA catabolic process, non-stop decay                                                                                                                                                                                                                                                                                    
The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.                                                                                                                                                                                             
	
80219
GO:0071432                                                                                                                                                                                                                                                                                                                                    
peptide mating pheromone maturation involved in conjugation with cellular fusion                                                                                                                                                                                                                                                              
The formation of a mature peptide mating pheromone by proteolysis and/or modification of a peptide precursor, occurring in the context of conjugation with cellular fusion.                                                                                                                                                                   
	
80494
GO:0071586                                                                                                                                                                                                                                                                                                                                    
CAAX-box protein processing                                                                                                                                                                                                                                                                                                                   
The second process in a series of specific posttranslational modifications to the CAAX box region of CAAX box proteins, in which the last three amino acids of the protein (AAX) are removed by proteolysis.                                                                                                                                  



	
$`32`
		

go_id
Term
Definition

	
359
GO:0000147                                                                                                                                                                                                                                                                                      
actin cortical patch assembly                                                                                                                                                                                                                                                                   
Assembly of an actin cortical patch, a discrete actin-containing structure found at the plasma membrane of fungal cells.                                                                                                                                                                        
	
16856
GO:0006995                                                                                                                                                                                                                                                                                      
cellular response to nitrogen starvation                                                                                                                                                                                                                                                        
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.                                                                                                         
	
16965
GO:0007064                                                                                                                                                                                                                                                                                      
mitotic sister chromatid cohesion                                                                                                                                                                                                                                                               
The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission.
	
18415
GO:0043066                                                                                                                                                                                                                                                                                      
negative regulation of apoptotic process                                                                                                                                                                                                                                                        
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.                                                                                                                                                                                  
	
19499
GO:0030041                                                                                                                                                                                                                                                                                      
actin filament polymerization                                                                                                                                                                                                                                                                   
Assembly of actin filaments by the addition of actin monomers to a filament.                                                                                                                                                                                                                    
	
24225
GO:0010508                                                                                                                                                                                                                                                                                      
positive regulation of autophagy                                                                                                                                                                                                                                                                
Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.                                                                                                                                          
	
26465
GO:0015824                                                                                                                                                                                                                                                                                      
proline transport                                                                                                                                                                                                                                                                               
The directed movement of proline, pyrrolidine-2-carboxylic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                         
	
26481
GO:0015840                                                                                                                                                                                                                                                                                      
urea transport                                                                                                                                                                                                                                                                                  
The directed movement of urea into, out of or within the cell. Urea is the water-soluble compound H2N-CO-NH2.                                                                                                                                                                                   
	
27793
GO:0016579                                                                                                                                                                                                                                                                                      
protein deubiquitination                                                                                                                                                                                                                                                                        
The removal of one or more ubiquitin groups from a protein.                                                                                                                                                                                                                                     
	
37648
GO:0031929                                                                                                                                                                                                                                                                                      
TOR signaling                                                                                                                                                                                                                                                                                   
A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors.                                           
	
37819
GO:0032007                                                                                                                                                                                                                                                                                      
negative regulation of TOR signaling                                                                                                                                                                                                                                                            
Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.                                                                                                                                                                                                    
	
43227
GO:0034087                                                                                                                                                                                                                                                                                      
establishment of mitotic sister chromatid cohesion                                                                                                                                                                                                                                              
The process in which the sister chromatids of a replicated chromosome become joined along the entire length of the chromosome during S phase during a mitotic cell cycle.                                                                                                                       
	
52140
GO:0043558                                                                                                                                                                                                                                                                                      
regulation of translational initiation in response to stress                                                                                                                                                                                                                                    
Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating the organism is under stress.                                                                                                                                          
	
53678
GO:0044376                                                                                                                                                                                                                                                                                      
RNA polymerase II complex import to nucleus                                                                                                                                                                                                                                                     
The directed movement of the DNA-directed RNA polymerase II core complex from the cytoplasm into the nucleus.                                                                                                                                                                                   
	
104321
GO:1902499                                                                                                                                                                                                                                                                                      
positive regulation of protein autoubiquitination                                                                                                                                                                                                                                               
Any process that activates or increases the frequency, rate or extent of protein autoubiquitination.                                                                                                                                                                                            
	
115186
GO:1903833                                                                                                                                                                                                                                                                                      
positive regulation of cellular response to amino acid starvation                                                                                                                                                                                                                               
Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.                                                                                                                                                                            
	
129962
GO:1990022                                                                                                                                                                                                                                                                                      
RNA polymerase III complex localization to nucleus                                                                                                                                                                                                                                              
The directed movement of an RNA polymerase III complex from the cytoplasm to the nucleus.                                                                                                                                                                                                       
	
132956
GO:2000785                                                                                                                                                                                                                                                                                      
regulation of autophagosome assembly                                                                                                                                                                                                                                                            
Any process that modulates the frequency, rate or extent of autophagosome assembly.                                                                                                                                                                                                             



	
$`33`
		

go_id
Term
Definition

	
1835
GO:0001174                                                                                                                                                                                                                                                        
transcriptional start site selection at RNA polymerase II promoter                                                                                                                                                                                                
Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.             
	
15379
GO:0006356                                                                                                                                                                                                                                                        
regulation of transcription from RNA polymerase I promoter                                                                                                                                                                                                        
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.                                                                                                                                                      
	
16606
GO:0006855                                                                                                                                                                                                                                                        
drug transmembrane transport                                                                                                                                                                                                                                      
The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.                                                                                                                         
	
34125
GO:0030261                                                                                                                                                                                                                                                        
chromosome condensation                                                                                                                                                                                                                                           
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.                                                                                  
	
45323
GO:0035376                                                                                                                                                                                                                                                        
sterol import                                                                                                                                                                                                                                                     
The directed movement of a sterol into a cell or organelle. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.                                                                                                   
	
45830
GO:0035690                                                                                                                                                                                                                                                        
cellular response to drug                                                                                                                                                                                                                                         
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	
69919
GO:0051123                                                                                                                                                                                                                                                        
RNA polymerase II transcriptional preinitiation complex assembly                                                                                                                                                                                                  
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.                         
	
76503
GO:0060962                                                                                                                                                                                                                                                        
regulation of ribosomal protein gene transcription from RNA polymerase II promoter                                                                                                                                                                                
Any process that modulates the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter.                                                                                 
	
84061
GO:0090579                                                                                                                                                                                                                                                        
dsDNA loop formation                                                                                                                                                                                                                                              
The formation and maintenance of DNA loops that juxtapose separated regions on the same dsDNA molecule.                                                                                                                                                           



	
$`34`
		

go_id
Term
Definition

	
211
GO:0000086                                                                                                                                                                                                                                                                                                                                                      
G2/M transition of mitotic cell cycle                                                                                                                                                                                                                                                                                                                           
The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	
522
GO:0000209                                                                                                                                                                                                                                                                                                                                                      
protein polyubiquitination                                                                                                                                                                                                                                                                                                                                      
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.                                                                                                                                                                                                                                                                                  
	
549
GO:0042787                                                                                                                                                                                                                                                                                                                                                      
protein ubiquitination involved in ubiquitin-dependent protein catabolic process                                                                                                                                                                                                                                                                                
The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.                                                                                                                                                                                                  
	
14821
GO:0006122                                                                                                                                                                                                                                                                                                                                                      
mitochondrial electron transport, ubiquinol to cytochrome c                                                                                                                                                                                                                                                                                                     
The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.                                                                                                                                                                                                
	
15905
GO:0006611                                                                                                                                                                                                                                                                                                                                                      
protein export from nucleus                                                                                                                                                                                                                                                                                                                                     
The directed movement of a protein from the nucleus into the cytoplasm.                                                                                                                                                                                                                                                                                         
	
26754
GO:0016024                                                                                                                                                                                                                                                                                                                                                      
CDP-diacylglycerol biosynthetic process                                                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways resulting in the formation of CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate.                                                                                                                                                           
	
36120
GO:0031146                                                                                                                                                                                                                                                                                                                                                      
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process                                                                                                                                                                                                                                                                                         
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome.                                                            
	
37914
GO:0032049                                                                                                                                                                                                                                                                                                                                                      
cardiolipin biosynthetic process                                                                                                                                                                                                                                                                                                                                
The chemical reactions and pathways resulting in the formation of cardiolipin, 1,3-bis(3-phosphatidyl)glycerol.                                                                                                                                                                                                                                                 
	
41723
GO:0033617                                                                                                                                                                                                                                                                                                                                                      
mitochondrial respiratory chain complex IV assembly                                                                                                                                                                                                                                                                                                             
The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase) in the mitochondrial inner membrane.                                                                                                                                                                         
	
70542
GO:0051301                                                                                                                                                                                                                                                                                                                                                      
cell division                                                                                                                                                                                                                                                                                                                                                   
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                                                                                  
	
72246
GO:0051865                                                                                                                                                                                                                                                                                                                                                      
protein autoubiquitination                                                                                                                                                                                                                                                                                                                                      
The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.                                                                                                                                                        
	
77786
GO:0070202                                                                                                                                                                                                                                                                                                                                                      
regulation of establishment of protein localization to chromosome                                                                                                                                                                                                                                                                                               
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome.                                                                                                                                                                                                                          



	
$`35`
		

go_id
Term
Definition




	
$`36`
		

go_id
Term
Definition

	
14489
GO:0006006                                                                                                                                                                                                                                                                                                                              
glucose metabolic process                                                                                                                                                                                                                                                                                                               
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.                            
	
22623
GO:0009651                                                                                                                                                                                                                                                                                                                              
response to salt stress                                                                                                                                                                                                                                                                                                                 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
	
80502
GO:0071590                                                                                                                                                                                                                                                                                                                              
nicotinamide riboside biosynthetic process                                                                                                                                                                                                                                                                                              
The chemical reactions and pathways resulting in the formation of nicotinamide riboside, the product of the formation of a glycosidic bond between ribose and nicotinamide.                                                                                                                                                             
	
80509
GO:0071592                                                                                                                                                                                                                                                                                                                              
nicotinic acid riboside biosynthetic process                                                                                                                                                                                                                                                                                            
The chemical reactions and pathways resulting in the formation of nicotinic acid riboside, the product of the formation of a glycosidic bond between ribose and nicotinic acid.                                                                                                                                                         



	
$`37`
		

go_id
Term
Definition

	
456
GO:0000183                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
chromatin silencing at rDNA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
Repression of transcription of ribosomal DNA by altering the structure of chromatin.                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
1247
GO:0000706                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
meiotic DNA double-strand break processing                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The cell cycle process in which the 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang occurs. This takes place during meiosis.                                                                                                                                                                                                                                                                                                                            
	
1308
GO:0000737                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
DNA catabolic process, endonucleolytic                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.                                                                                                                                                                                                                                                                                                                                 
	
5895
GO:0003333                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
amino acid transmembrane transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
The directed movement of amino acids, organic acids containing one or more amino substituents across a membrane by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                                                 
	
15684
GO:0006535                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
cysteine biosynthetic process from serine                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.                                                                                                                                                                                                                                                                                                                                                                                                    
	
17020
GO:0007089                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
traversing start control point of mitotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
A cell cycle process by which a cell commits to entering S phase via a positive feedback mechanism between the regulation of transcription and G1 CDK activity.                                                                                                                                                                                                                                                                                                                                                       
	
24566
GO:0010791                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
DNA double-strand break processing involved in repair via synthesis-dependent strand annealing                                                                                                                                                                                                                                                                                                                                                                                                                        
The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang that results in the repair of a double strand break via synthesis-dependent strand annealing.                                                                                                                                                                                                                                                                                                       
	
26468
GO:0015827                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
tryptophan transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The directed movement of tryptophan, 2-amino-3-(1H-indol-3-yl)propanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                                  
	
31295
GO:0019343                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
cysteine biosynthetic process via cystathionine                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The chemical reactions and pathways resulting in the formation of cysteine, via the intermediate cystathionine.                                                                                                                                                                                                                                                                                                                                                                                                       
	
31307
GO:0019346                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
transsulfuration                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes.                                                                                                                                                                                                                                                                                                 
	
36404
GO:0031292                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
gene conversion at mating-type locus, DNA double-strand break processing                                                                                                                                                                                                                                                                                                                                                                                                                                              
The 5' to 3' exonucleolytic resection of the DNA at the site of the break at the mating-type locus to form a 3' single-strand DNA overhang.                                                                                                                                                                                                                                                                                                                                                                           
	
37553
GO:0031860                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
telomeric 3' overhang formation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The formation of the single stranded telomeric 3' overhang, a conserved feature that ranges in length from 12 nt in budding yeast to approximately 500 nt in humans.                                                                                                                                                                                                                                                                                                                                                  
	
44024
GO:0034503                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
protein localization to nucleolar rDNA repeats                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process in which a protein is transported to, or maintained at, the rDNA repeats on a chromosome in the nucleolus.                                                                                                                                                                                                                                                                                                                                                                                                
	
48672
GO:0042138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
meiotic DNA double-strand break formation                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The cell cycle process in which double-strand breaks are generated at defined hotspots throughout the genome during meiosis I. This results in the initiation of meiotic recombination.                                                                                                                                                                                                                                                                                                                               
	
54648
GO:0045143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
homologous chromosome segregation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the first division of the meiotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner; this pairing off, referred to as synapsis, permits genetic recombination. One homolog (both sister chromatids) of each morphologic type goes into each of the resulting chromosome sets.
	
78651
GO:0070550                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
rDNA condensation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The process in which the chromatin structure of the rDNA repeats is compacted. In S. cerevisiae, condensation and resolution of the rDNA occurs during anaphase.                                                                                                                                                                                                                                                                                                                                                      
	
79201
GO:0070814                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
hydrogen sulfide biosynthetic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.                                                                                                                                                                                                                                                                                                                                                                                                                              
	
83735
GO:0090282                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
positive regulation of transcription involved in G2/M transition of mitotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                                                
Any process that activates or increases the frequency, rate or extent of transcription of target genes that are transcribed as part of the G2/M transition of the mitotic cell cycle.                                                                                                                                                                                                                                                                                                                                 



	
$`38`
		

go_id
Term
Definition

	
1349
GO:0000754                                                                                                                                                                                                                                                                                                                                                
adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion                                                                                                                                                                                                                                                     
In organisms that undergo conjugation with cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses. An example of this is the adaptation to pheromone during conjugation with cellular fusion in Saccharomyces cerevisiae.
	
2441
GO:0001731                                                                                                                                                                                                                                                                                                                                                
formation of translation preinitiation complex                                                                                                                                                                                                                                                                                                            
The joining of the small ribosomal subunit, ternary complex, and mRNA.                                                                                                                                                                                                                                                                                    
	
5987
GO:0003400                                                                                                                                                                                                                                                                                                                                                
regulation of COPII vesicle coating                                                                                                                                                                                                                                                                                                                       
Any process that modulates the rate, frequency, or extent of the addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.                                                                                                                                                      
	
15518
GO:0006446                                                                                                                                                                                                                                                                                                                                                
regulation of translational initiation                                                                                                                                                                                                                                                                                                                    
Any process that modulates the frequency, rate or extent of translational initiation.                                                                                                                                                                                                                                                                     
	
16799
GO:0006972                                                                                                                                                                                                                                                                                                                                                
hyperosmotic response                                                                                                                                                                                                                                                                                                                                     
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.                             
	
17055
GO:0007120                                                                                                                                                                                                                                                                                                                                                
axial cellular bud site selection                                                                                                                                                                                                                                                                                                                         
The process of defining the next site of bud emergence adjacent to the last site of bud emergence on a budding cell.                                                                                                                                                                                                                                      
	
17057
GO:0007121                                                                                                                                                                                                                                                                                                                                                
bipolar cellular bud site selection                                                                                                                                                                                                                                                                                                                       
The process of defining subsequent sites of bud emergence such that budding takes place at alternating poles of a budding cell.                                                                                                                                                                                                                           
	
17324
GO:0007231                                                                                                                                                                                                                                                                                                                                                
osmosensory signaling pathway                                                                                                                                                                                                                                                                                                                             
The series of molecular signals initiated in response to osmotic change.                                                                                                                                                                                                                                                                                  
	
23338
GO:0009967                                                                                                                                                                                                                                                                                                                                                
positive regulation of signal transduction                                                                                                                                                                                                                                                                                                                
Any process that activates or increases the frequency, rate or extent of signal transduction.                                                                                                                                                                                                                                                             
	
27327
GO:0016241                                                                                                                                                                                                                                                                                                                                                
regulation of macroautophagy                                                                                                                                                                                                                                                                                                                              
Any process that modulates the frequency, rate or extent of macroautophagy.                                                                                                                                                                                                                                                                               
	
28765
GO:0046685                                                                                                                                                                                                                                                                                                                                                
response to arsenic-containing substance                                                                                                                                                                                                                                                                                                                  
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.                                                                       
	
36891
GO:0031505                                                                                                                                                                                                                                                                                                                                                
fungal-type cell wall organization                                                                                                                                                                                                                                                                                                                        
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.                                                                                                                                                                                         
	
40931
GO:0033262                                                                                                                                                                                                                                                                                                                                                
regulation of nuclear cell cycle DNA replication                                                                                                                                                                                                                                                                                                          
Any process that modulates the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.                                                                                                                                                                               
	
43640
GO:0034316                                                                                                                                                                                                                                                                                                                                                
negative regulation of Arp2/3 complex-mediated actin nucleation                                                                                                                                                                                                                                                                                           
Any process that stops, prevents, or reduces the frequency, rate or extent of actin nucleation mediated by the Arp2/3 complex and interacting proteins.                                                                                                                                                                                                   
	
76988
GO:0061393                                                                                                                                                                                                                                                                                                                                                
positive regulation of transcription from RNA polymerase II promoter in response to osmotic stress                                                                                                                                                                                                                                                        
Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.                                                                                                                   
	
130128
GO:1990145                                                                                                                                                                                                                                                                                                                                                
maintenance of translational fidelity                                                                                                                                                                                                                                                                                                                     
Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template.                                                                                                                                                                                         



	
$`39`
		

go_id
Term
Definition

	
14983
GO:0006177                                                                                                                                                                                                                               
GMP biosynthetic process                                                                                                                                                                                                                 
The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.                                                                                                                                          
	
14998
GO:0006183                                                                                                                                                                                                                               
GTP biosynthetic process                                                                                                                                                                                                                 
The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.                                                                                                                                           
	
27785
GO:0016573                                                                                                                                                                                                                               
histone acetylation                                                                                                                                                                                                                      
The modification of a histone by the addition of an acetyl group.                                                                                                                                                                        
	
69919
GO:0051123                                                                                                                                                                                                                               
RNA polymerase II transcriptional preinitiation complex assembly                                                                                                                                                                         
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.



	
$`40`
		

go_id
Term
Definition

	
211
GO:0000086                                                                                                                                                                                                                                                                                                                                                      
G2/M transition of mitotic cell cycle                                                                                                                                                                                                                                                                                                                           
The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	
1254
GO:0000710                                                                                                                                                                                                                                                                                                                                                      
meiotic mismatch repair                                                                                                                                                                                                                                                                                                                                         
A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules. Correction of the mismatch can result in non-Mendelian segregation of alleles following meiosis.                                           
	
32571
GO:0019918                                                                                                                                                                                                                                                                                                                                                      
peptidyl-arginine methylation, to symmetrical-dimethyl arginine                                                                                                                                                                                                                                                                                                 
The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N'(omega)-dimethyl-L-arginine.                                                                                                                                                                                                                                                        
	
44678
GO:0034969                                                                                                                                                                                                                                                                                                                                                      
histone arginine methylation                                                                                                                                                                                                                                                                                                                                    
The modification of a histone by addition of a methyl group to an arginine residue.                                                                                                                                                                                                                                                                             
	
69680
GO:0051026                                                                                                                                                                                                                                                                                                                                                      
chiasma assembly                                                                                                                                                                                                                                                                                                                                                
The cell cycle process in which a connection between chromatids assembles, indicating where an exchange of homologous segments has taken place by the crossing-over of non-sister chromatids.                                                                                                                                                                   
	
69919
GO:0051123                                                                                                                                                                                                                                                                                                                                                      
RNA polymerase II transcriptional preinitiation complex assembly                                                                                                                                                                                                                                                                                                
The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.                                                                                                                       



	
$`41`
		

go_id
Term
Definition

	
313
GO:0000122                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
negative regulation of transcription from RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
	
549
GO:0042787                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
protein ubiquitination involved in ubiquitin-dependent protein catabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
1283
GO:0000723                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
telomere maintenance                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.                                                                                                                                                                                                                                                                   
	
1296
GO:0000730                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
DNA recombinase assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
1918
GO:0001308                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
negative regulation of chromatin silencing involved in replicative cell aging                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins.                                                                                                                                                                                                                                                                                                                                                                                                                                                
	
14761
GO:0006099                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
tricarboxylic acid cycle                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.                                                                                     
	
14765
GO:0006103                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
2-oxoglutarate metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.                                                                                                                                                                                                                                                                                                                                                                                                                   
	
15267
GO:0006281                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
DNA repair                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	
24353
GO:0010621                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
negative regulation of transcription by transcription factor localization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor.                                                                                                                                                                                                                                                                                                                                                                                                                      
	
24851
GO:0010978                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
gene silencing involved in chronological cell aging                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any transcriptional or post-transcriptional process, arising in non-dividing cells as they age, carried out at the cellular level that results in long-term gene inactivation.                                                                                                                                                                                                                                                                                                                                                                                                                             
	
27788
GO:0016575                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
histone deacetylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
The modification of histones by removal of acetyl groups.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
28375
GO:0016925                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
protein sumoylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.                                                                                                                                                                                                                                                                                                                                                               
	
35913
GO:0031047                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
gene silencing by RNA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process in which RNA molecules inactivate expression of target genes.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
37687
GO:0031938                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
regulation of chromatin silencing at telomere                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process that affects the rate, extent or location of chromatin silencing at telomeres.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
	
40884
GO:0033234                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
negative regulation of protein sumoylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of SUMO groups to a protein.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
	
41496
GO:0033512                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
L-lysine catabolic process to acetyl-CoA via saccharopine                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate saccharopine.                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
50814
GO:0043007                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
maintenance of rDNA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process involved in sustaining the fidelity and copy number of rDNA repeats.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
70917
GO:0051438                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
regulation of ubiquitin-protein transferase activity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that modulates the frequency, rate or extent of ubiquitin transferase activity.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
	
71046
GO:0051457                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
maintenance of protein location in nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus.                                                                                                                                                                                                                                                                                                                                        
	
83755
GO:0090295                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
nitrogen catabolite repression of transcription                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.                                                                                                                                                                                                                                                                                                                                                                             



	
$`42`
		

go_id
Term
Definition

	
883
GO:0000301                                                                                                                                                                                                                                                                                                                                                                                                                                                               
retrograde transport, vesicle recycling within Golgi                                                                                                                                                                                                                                                                                                                                                                                                                     
The retrograde movement of substances within the Golgi, mediated by COP I vesicles. Cis-Golgi vesicles are constantly moving forward through the Golgi stack by cisternal progression, eventually becoming trans-Golgi vesicles. They then selectively transport membrane and luminal proteins from the trans- to the medial-Golgi while leaving others behind in the trans-Golgi cisternae; similarly, they selectively move proteins from the medial- to the cis-Golgi.
	
16509
GO:0006797                                                                                                                                                                                                                                                                                                                                                                                                                                                               
polyphosphate metabolic process                                                                                                                                                                                                                                                                                                                                                                                                                                          
The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.                                                                                                                                                                                                                                                                                                                                                                 
	
16669
GO:0006890                                                                                                                                                                                                                                                                                                                                                                                                                                                               
retrograde vesicle-mediated transport, Golgi to ER                                                                                                                                                                                                                                                                                                                                                                                                                       
The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.                                                                                                                                                                                                                                                                                                           
	
16919
GO:0007030                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Golgi organization                                                                                                                                                                                                                                                                                                                                                                                                                                                       
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.                                                                                                                                                                                                                                                                                                              
	
16926
GO:0007034                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuolar transport                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The directed movement of substances into, out of or within a vacuole.                                                                                                                                                                                                                                                                                                                                                                                                    
	
16927
GO:0007035                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuolar acidification                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion.                                                                                                                                                                                                                                                                                                                                                                       
	
26722
GO:0015991                                                                                                                                                                                                                                                                                                                                                                                                                                                               
ATP hydrolysis coupled proton transport                                                                                                                                                                                                                                                                                                                                                                                                                                  
The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.                                                                                                                                                                                                                                                                                                                                                                          
	
27319
GO:0016237                                                                                                                                                                                                                                                                                                                                                                                                                                                               
lysosomal microautophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                 
The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.                                                                         
	
34090
GO:0030242                                                                                                                                                                                                                                                                                                                                                                                                                                                               
pexophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions.                                                                                                                                                                                                                                                                                                                                                  
	
38427
GO:0032258                                                                                                                                                                                                                                                                                                                                                                                                                                                               
CVT pathway                                                                                                                                                                                                                                                                                                                                                                                                                                                              
A constitutive biosynthetic process that occurs under nutrient-rich conditions, in which two resident vacuolar hydrolases, aminopeptidase I and alpha-mannosidase, are sequestered into vesicles; these vesicles are transported to, and then fuse with, the vacuole. This pathway is mostly observed in yeast.                                                                                                                                                          
	
48677
GO:0042144                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuole fusion, non-autophagic                                                                                                                                                                                                                                                                                                                                                                                                                                           
The fusion of two vacuole membranes to form a single vacuole.                                                                                                                                                                                                                                                                                                                                                                                                            
	
65071
GO:0048213                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Golgi vesicle prefusion complex stabilization                                                                                                                                                                                                                                                                                                                                                                                                                            
The binding of specific proteins to the t-SNARE/v-SNARE/SNAP25 complex, by which the Golgi vesicle prefusion complex is stabilized.                                                                                                                                                                                                                                                                                                                                      
	
77582
GO:0070072                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuolar proton-transporting V-type ATPase complex assembly                                                                                                                                                                                                                                                                                                                                                                                                              
The aggregation, arrangement and bonding together of a vacuolar proton-transporting V-type ATPase complex, proton-transporting two-sector ATPase complex that couples ATP hydrolysis to the transport of protons across the vacuolar membrane.                                                                                                                                                                                                                           



	
$`43`
		

go_id
Term
Definition

	
97
GO:0000045                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
autophagosome assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
883
GO:0000301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
retrograde transport, vesicle recycling within Golgi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
The retrograde movement of substances within the Golgi, mediated by COP I vesicles. Cis-Golgi vesicles are constantly moving forward through the Golgi stack by cisternal progression, eventually becoming trans-Golgi vesicles. They then selectively transport membrane and luminal proteins from the trans- to the medial-Golgi while leaving others behind in the trans-Golgi cisternae; similarly, they selectively move proteins from the medial- to the cis-Golgi.                                                                                                                                                                                                                                                                                                                    
	
1129
GO:0000422                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
mitophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
	
16656
GO:0006888                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
ER to Golgi vesicle-mediated transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
27314
GO:0016236                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
macroautophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure.  Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	
34090
GO:0030242                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
pexophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
	
38193
GO:0032147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
activation of protein kinase activity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Any process that initiates the activity of an inactive protein kinase.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
	
38427
GO:0032258                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
CVT pathway                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
A constitutive biosynthetic process that occurs under nutrient-rich conditions, in which two resident vacuolar hydrolases, aminopeptidase I and alpha-mannosidase, are sequestered into vesicles; these vesicles are transported to, and then fuse with, the vacuole. This pathway is mostly observed in yeast.                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
	
44374
GO:0034727                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
piecemeal microautophagy of nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
Degradation of a cell nucleus by lysosomal microautophagy.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
	
54185
GO:0044805                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
late nucleophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  



	
$`44`
		

go_id
Term
Definition

	
1354
GO:0000755                                                                                                                                                                                                                                                                                                                                                                                                                        
cytogamy                                                                                                                                                                                                                                                                                                                                                                                                                          
During conjugation with cellular fusion, the process resulting in creating a single cell from complementary mating types. The localized remodeling and dissolution of external protective structures allow the fusion of the plasma membranes and cytoplasmic mixing. An example of this process is found in Saccharomyces cerevisiae.                                                                                            
	
1737
GO:0001100                                                                                                                                                                                                                                                                                                                                                                                                                        
negative regulation of exit from mitosis                                                                                                                                                                                                                                                                                                                                                                                          
Any process involved in the inhibition of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).                                                                                                                                                                                                                                                                                       
	
18733
GO:0008360                                                                                                                                                                                                                                                                                                                                                                                                                        
regulation of cell shape                                                                                                                                                                                                                                                                                                                                                                                                          
Any process that modulates the surface configuration of a cell.                                                                                                                                                                                                                                                                                                                                                                   
	
27304
GO:0016226                                                                                                                                                                                                                                                                                                                                                                                                                        
iron-sulfur cluster assembly                                                                                                                                                                                                                                                                                                                                                                                                      
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.                                                                                                                                                                                                                                                                                                                                                     
	
38876
GO:0032465                                                                                                                                                                                                                                                                                                                                                                                                                        
regulation of cytokinesis                                                                                                                                                                                                                                                                                                                                                                                                         
Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.                                                                                                                                                                                                                                                                                   
	
76127
GO:0060627                                                                                                                                                                                                                                                                                                                                                                                                                        
regulation of vesicle-mediated transport                                                                                                                                                                                                                                                                                                                                                                                          
Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.                                                                                                                                                                                                                  
	
83798
GO:0090337                                                                                                                                                                                                                                                                                                                                                                                                                        
regulation of formin-nucleated actin cable assembly                                                                                                                                                                                                                                                                                                                                                                               
Any process that modulates the rate, frequency, or extent of formin-nucleated actin cable assembly. Formin-nucleated actin cable assembly is the aggregation, arrangement and bonding together of a set of components to form a formin-nucleated actin cable. A formin-nucleated actin cable is an actin filament bundle that consists of short filaments organized into bundles of uniform polarity, and is nucleated by formins.



	
$`45`
		

go_id
Term
Definition

	
15619
GO:0016485                                                                                                                                                                                                                                                                                                                                                                                                                                                           
protein processing                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.                                                                                                                                                                                                                                                       
	
16652
GO:0006887                                                                                                                                                                                                                                                                                                                                                                                                                                                           
exocytosis                                                                                                                                                                                                                                                                                                                                                                                                                                                           
A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This process begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when vesicle fusion is complete. This is the process in which most molecules are secreted from eukaryotic cells.
	
16656
GO:0006888                                                                                                                                                                                                                                                                                                                                                                                                                                                           
ER to Golgi vesicle-mediated transport                                                                                                                                                                                                                                                                                                                                                                                                                               
The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.                                                                                                                                                                                   
	
16711
GO:0006914                                                                                                                                                                                                                                                                                                                                                                                                                                                           
autophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.                                                                                                                                                                                                                                    
	
26819
GO:0016050                                                                                                                                                                                                                                                                                                                                                                                                                                                           
vesicle organization                                                                                                                                                                                                                                                                                                                                                                                                                                                 
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.                                                                                                                                                                                                                                                                                                                    
	
34437
GO:0030433                                                                                                                                                                                                                                                                                                                                                                                                                                                           
ER-associated ubiquitin-dependent protein catabolic process                                                                                                                                                                                                                                                                                                                                                                                                          
The chemical reactions and pathways resulting in the breakdown of proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation. This process acts on misfolded proteins as well as in the regulated degradation of correctly folded proteins.                                                                                                                                                                         
	
36887
GO:0031503                                                                                                                                                                                                                                                                                                                                                                                                                                                           
protein complex localization                                                                                                                                                                                                                                                                                                                                                                                                                                         
A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.                                                                                                                                                                                                                                                                                                                                         
	
38427
GO:0032258                                                                                                                                                                                                                                                                                                                                                                                                                                                           
CVT pathway                                                                                                                                                                                                                                                                                                                                                                                                                                                          
A constitutive biosynthetic process that occurs under nutrient-rich conditions, in which two resident vacuolar hydrolases, aminopeptidase I and alpha-mannosidase, are sequestered into vesicles; these vesicles are transported to, and then fuse with, the vacuole. This pathway is mostly observed in yeast.                                                                                                                                                      
	
60341
GO:0046777                                                                                                                                                                                                                                                                                                                                                                                                                                                           
protein autophosphorylation                                                                                                                                                                                                                                                                                                                                                                                                                                          
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).                                                                                                                                                                                                                                                                                           



	
$`46`
		

go_id
Term
Definition

	
16931
GO:0007039                                                                                                                              
protein catabolic process in the vacuole                                                                                                
The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.



	
$`47`
		

go_id
Term
Definition

	
1718
GO:0001081                                                                                                                                                                                                                                                         
nitrogen catabolite repression of transcription from RNA polymerase II promoter                                                                                                                                                                                    
A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	
15335
GO:0006338                                                                                                                                                                                                                                                         
chromatin remodeling                                                                                                                                                                                                                                               
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.                       
	
16982
GO:0007070                                                                                                                                                                                                                                                         
negative regulation of transcription from RNA polymerase II promoter during mitosis                                                                                                                                                                                
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter during mitosis.                                                                                                                     
	
17060
GO:0007124                                                                                                                                                                                                                                                         
pseudohyphal growth                                                                                                                                                                                                                                                
A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate.         
	
23079
GO:0009847                                                                                                                                                                                                                                                         
spore germination                                                                                                                                                                                                                                                  
The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall).                                                                                           
	
24420
GO:0010673                                                                                                                                                                                                                                                         
positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle                                                                                                                                                                
A cell cycle process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as part of the meiotic cell cycle.                                                                                                           
	
24421
GO:0010674                                                                                                                                                                                                                                                         
negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle                                                                                                                                                                
A cell cycle process that decreases the frequency, rate or extent of transcription from an RNA polymerase II as part of the meiotic cell cycle.                                                                                                                    
	
27782
GO:0016569                                                                                                                                                                                                                                                         
chromatin modification                                                                                                                                                                                                                                             
The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups.                                                                                                                                                              
	
43800
GO:0034389                                                                                                                                                                                                                                                         
lipid particle organization                                                                                                                                                                                                                                        
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle.                                                                                                           
	
90476
GO:1900471                                                                                                                                                                                                                                                         
negative regulation of inositol biosynthetic process by negative regulation of transcription from RNA polymerase II promoter                                                                                                                                       
Any process that stops, prevents, or reduces the frequency, rate or extent of inositol biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                
	
90484
GO:1900472                                                                                                                                                                                                                                                         
positive regulation of phosphatidylcholine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter                                                                                                                            
Any process that activates or increases the frequency, rate or extent of phosphatidylcholine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                   
	
90493
GO:1900475                                                                                                                                                                                                                                                         
positive regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter                                                                                                                                                             
Any process that activates or increases the frequency, rate or extent of meiosis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                           
	
90498
GO:1900476                                                                                                                                                                                                                                                         
positive regulation of meiosis by positive regulation of transcription from RNA polymerase II promoter                                                                                                                                                             
Any process that activates or increases the frequency, rate or extent of meiosis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                                                    
	
90910
GO:1900525                                                                                                                                                                                                                                                         
positive regulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter                                                                                                                             
Any process that activates or increases the frequency, rate or extent of phosphatidylserine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.                                    



	
$`48`
		

go_id
Term
Definition

	
15932
GO:0006620                                                                                                                                                                                                                                                                                                                                                                                                                   
posttranslational protein targeting to membrane                                                                                                                                                                                                                                                                                                                                                                              
The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane.
	
16669
GO:0006890                                                                                                                                                                                                                                                                                                                                                                                                                   
retrograde vesicle-mediated transport, Golgi to ER                                                                                                                                                                                                                                                                                                                                                                           
The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.                                                                                                                                                                                                                                                               
	
16968
GO:0007067                                                                                                                                                                                                                                                                                                                                                                                                                   
mitotic nuclear division                                                                                                                                                                                                                                                                                                                                                                                                     
A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.                                                                                                                       
	
17380
GO:0007266                                                                                                                                                                                                                                                                                                                                                                                                                   
Rho protein signal transduction                                                                                                                                                                                                                                                                                                                                                                                              
A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.                                                                                                                                                                                                                                                                             
	
27731
GO:0016560                                                                                                                                                                                                                                                                                                                                                                                                                   
protein import into peroxisome matrix, docking                                                                                                                                                                                                                                                                                                                                                                               
The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.                                                                                                                                                                                                                                       
	
34090
GO:0030242                                                                                                                                                                                                                                                                                                                                                                                                                   
pexophagy                                                                                                                                                                                                                                                                                                                                                                                                                    
The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions.                                                                                                                                                                                                                                                                                                      
	
54345
GO:0045048                                                                                                                                                                                                                                                                                                                                                                                                                   
protein insertion into ER membrane                                                                                                                                                                                                                                                                                                                                                                                           
The process that results in incorporation of a protein into an endoplasmic reticulum (ER) membrane. It depends on specific topogenic sequences of amino acids that ensure that a protein acquires the proper orientation during its insertion into the ER membrane.                                                                                                                                                          
	
70542
GO:0051301                                                                                                                                                                                                                                                                                                                                                                                                                   
cell division                                                                                                                                                                                                                                                                                                                                                                                                                
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                                                                                                                                               
	
70578
GO:0051321                                                                                                                                                                                                                                                                                                                                                                                                                   
meiotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                                           
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.                                                                                                                                                                                                               



	
$`49`
		

go_id
Term
Definition

	
1247
GO:0000706                                                                                                                                                                                                                                                                                                                                                                                                                                             
meiotic DNA double-strand break processing                                                                                                                                                                                                                                                                                                                                                                                                             
The cell cycle process in which the 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang occurs. This takes place during meiosis.                                                                                                                                                                                                                                                             
	
1283
GO:0000723                                                                                                                                                                                                                                                                                                                                                                                                                                             
telomere maintenance                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.                                                                                                               
	
1293
GO:0000727                                                                                                                                                                                                                                                                                                                                                                                                                                             
double-strand break repair via break-induced replication                                                                                                                                                                                                                                                                                                                                                                                               
The error-free repair of a double-strand break in DNA in which the centromere-proximal end of a broken chromosome searches for a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template, and progresses to the end of the chromosome.                                                                                                              
	
15273
GO:0006284                                                                                                                                                                                                                                                                                                                                                                                                                                             
base-excision repair                                                                                                                                                                                                                                                                                                                                                                                                                                   
In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.                                                                                                                                                                                                    
	
15295
GO:0006303                                                                                                                                                                                                                                                                                                                                                                                                                                             
double-strand break repair via nonhomologous end joining                                                                                                                                                                                                                                                                                                                                                                                               
The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	
17068
GO:0007131                                                                                                                                                                                                                                                                                                                                                                                                                                             
reciprocal meiotic recombination                                                                                                                                                                                                                                                                                                                                                                                                                       
The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.                                                   
	
24566
GO:0010791                                                                                                                                                                                                                                                                                                                                                                                                                                             
DNA double-strand break processing involved in repair via synthesis-dependent strand annealing                                                                                                                                                                                                                                                                                                                                                         
The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang that results in the repair of a double strand break via synthesis-dependent strand annealing.                                                                                                                                                                                                                                        
	
34452
GO:0030437                                                                                                                                                                                                                                                                                                                                                                                                                                             
ascospore formation                                                                                                                                                                                                                                                                                                                                                                                                                                    
The process in which cells that are products of meiosis acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota).                                                                                                                                                                 
	
37060
GO:0031573                                                                                                                                                                                                                                                                                                                                                                                                                                             
intra-S DNA damage checkpoint                                                                                                                                                                                                                                                                                                                                                                                                                          
A mitotic cell cycle checkpoint that slows DNA synthesis in response to DNA damage by the prevention of new origin firing and the stabilization of slow replication fork progression.                                                                                                                                                                                                                                                                  
	
45903
GO:0035753                                                                                                                                                                                                                                                                                                                                                                                                                                             
maintenance of DNA trinucleotide repeats                                                                                                                                                                                                                                                                                                                                                                                                               
Any process involved in sustaining the fidelity and copy number of DNA trinucleotide repeats. DNA trinucleotide repeats are naturally occurring runs of three base-pairs.                                                                                                                                                                                                                                                                              
	
48672
GO:0042138                                                                                                                                                                                                                                                                                                                                                                                                                                             
meiotic DNA double-strand break formation                                                                                                                                                                                                                                                                                                                                                                                                              
The cell cycle process in which double-strand breaks are generated at defined hotspots throughout the genome during meiosis I. This results in the initiation of meiotic recombination.                                                                                                                                                                                                                                                                
	
69691
GO:0051037                                                                                                                                                                                                                                                                                                                                                                                                                                             
regulation of transcription involved in meiotic cell cycle                                                                                                                                                                                                                                                                                                                                                                                             
Any process that modulates the frequency, rate or extent of transcription as part of a meiotic cell cycle.                                                                                                                                                                                                                                                                                                                                             
	
85058
GO:0097552                                                                                                                                                                                                                                                                                                                                                                                                                                             
mitochondrial double-strand break repair via homologous recombination                                                                                                                                                                                                                                                                                                                                                                                  
The repair of a double-strand break in mitochondrial DNA in which the broken DNA molecule is repaired using homologous sequences.                                                                                                                                                                                                                                                                                                                      



	
$`50`
		

go_id
Term
Definition

	
313
GO:0000122                                                                                                                     
negative regulation of transcription from RNA polymerase II promoter                                                           
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.



	
$`51`
		

go_id
Term
Definition

	
15892
GO:0006607                                                                                                                                                                                            
NLS-bearing protein import into nucleus                                                                                                                                                               
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.                                                      
	
17750
GO:0007533                                                                                                                                                                                            
mating type switching                                                                                                                                                                                 
The conversion of a single-cell organism from one mating type to another by the precise replacement of a DNA sequence at the expressed mating type locus with a copy of a sequence from a donor locus.
	
18613
GO:0008298                                                                                                                                                                                            
intracellular mRNA localization                                                                                                                                                                       
Any process in which mRNA is transported to, or maintained in, a specific location within the cell.                                                                                                   
	
24220
GO:0010499                                                                                                                                                                                            
proteasomal ubiquitin-independent protein catabolic process                                                                                                                                           
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome but do not involve ubiquitin.            
	
26717
GO:0015986                                                                                                                                                                                            
ATP synthesis coupled proton transport                                                                                                                                                                
The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.                                                                   
	
36105
GO:0031144                                                                                                                                                                                            
proteasome localization                                                                                                                                                                               
Any process in which the proteasome is transported to, or maintained in, a specific location.                                                                                                         
	
45947
GO:0035786                                                                                                                                                                                            
protein complex oligomerization                                                                                                                                                                       
The association of two or more multisubunit protein complexes to form dimers or other multimers of a protein complex.                                                                                 
	
49468
GO:0042407                                                                                                                                                                                            
cristae formation                                                                                                                                                                                     
The assembly of cristae, the inwards folds of the inner mitochondrial membrane.                                                                                                                       
	
60471
GO:0046839                                                                                                                                                                                            
phospholipid dephosphorylation                                                                                                                                                                        
The process of removing one or more phosphate groups from a phosphorylated lipid, any member of a group of substances soluble in lipid solvents but only sparingly soluble in aqueous solvents.       



	
$`52`
		

go_id
Term
Definition

	
143
GO:0000055                                                                                              
ribosomal large subunit export from nucleus                                                             
The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.                 
	
7108
GO:0006606                                                                                              
protein import into nucleus                                                                             
The directed movement of a protein from the cytoplasm to the nucleus.                                   
	
28410
GO:0016973                                                                                              
poly(A)+ mRNA export from nucleus                                                                       
The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.                           
	
70518
GO:0051292                                                                                              
nuclear pore complex assembly                                                                           
The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.

In [14]:

    

mapSimilarity <- function(mapID) {
    map <- getShortestPath(as.character(mapID))
    if (is.null(map)) return (NaN)
    communities <- sapply(rownames(map), function(rowname) getGenes(rowname))
    communitySimilarities <- mclusterSim(clusters = communities, semData = scGO, measure = "Wang", combine = "BMA")
    return(mean(communitySimilarities[upper.tri(communitySimilarities)]))
}


    

In [15]:

    

similarityOfAllMapsOnLayer <- function(layer) {
    mapSimilarities <- sapply(unique(assignments[,layer][assignments[,layer] != -1]), mapSimilarity)
    mapSimilarities <- mapSimilarities[!is.na(mapSimilarities)]
    return(mean(mapSimilarities))
}


    

In [16]:

    

layerMeanMapSimilarities <- sapply(colnames[1:length(colnames)-1], similarityOfAllMapsOnLayer)


    

    




Error in clusters[[i]]: subscript out of bounds
Traceback:

1. sapply(colnames[1:length(colnames) - 1], similarityOfAllMapsOnLayer)
2. sapply(colnames[1:length(colnames) - 1], similarityOfAllMapsOnLayer)
3. lapply(X = X, FUN = FUN, ...)
4. FUN(X[[i]], ...)
5. sapply(unique(assignments[, layer][assignments[, layer] != -1]), 
 .     mapSimilarity)   # at line 2 of file <text>
6. sapply(unique(assignments[, layer][assignments[, layer] != -1]), 
 .     mapSimilarity)
7. lapply(X = X, FUN = FUN, ...)
8. FUN(X[[i]], ...)
9. mclusterSim(clusters = communities, semData = scGO, measure = "Wang", 
 .     combine = "BMA")   # at line 5 of file <text>
10. sapply(clusters[[i]], gene2GO, semData, dropCodes = drop)
11. lapply(X = X, FUN = FUN, ...)

In [ ]:

    

sho


    

In [26]:

    

getShortestPath("1")


    

In [17]:

    

getNeighbours("4")


    

    




Error in map[com, ]: incorrect number of dimensions
Traceback:

1. getNeighbours("4")

In [62]:

    

numSharedTerms <- function(c1, c2) {
    return(length(intersect(names(enrichmentResults[["p-values", c1]]),
                            names(enrichmentResults[["p-values", c2]]))))
}


    

In [18]:

    

getShortestPath("1")


    

In [19]:

    

assignments


    

    






0
1

	
YGR046W
1 
34
	
YCL046W
1 
28
	
YJL030W
1 
24
	
YBR057C
1 
12
	
YKR026C
1 
16
	
YFL056C
1 
 7
	
YFL061W
1 
10
	
YDR174W
1 
33
	
YLR303W
1 
10
	
YPL211W
1 
 4
	
YOL020W
1 
37
	
YLR432W
1 
39
	
YPL229W
1 
 8
	
YMR236W
1 
21
	
YLR015W
1 
22
	
YCR050C
1 
14
	
YOR372C
1 
37
	
YLR046C
1 
41
	
YGR136W
1 
38
	
YJR072C
1 
32
	
YDR469W
1 
22
	
YBR196C
1 
 5
	
YHR140W
1 
 8
	
YDL088C
1 
17
	
YEL062W
1 
32
	
YJL178C
1 
 5
	
YKR037C
1 
 2
	
YNL047C
1 
 3
	
YLR113W
1 
38
	
YGR268C
1 
32
	
⋮
⋮
⋮
	
YOR264W
1 
38
	
YER116C
1 
41
	
YPL151C
1 
 2
	
YNL164C
1 
 8
	
YER027C
1 
12
	
YOR006C
1 
14
	
YDL013W
1 
41
	
YDR167W
1 
39
	
YNL023C
1 
50
	
YMR180C
1 
 9
	
YJL110C
1 
41
	
YNL199C
1 
 9
	
YHR057C
1 
 6
	
YFR002W
1 
52
	
YOR164C
1 
48
	
YLR291C
1 
26
	
YNR025C
1 
43
	
YGL025C
1 
40
	
YML114C
1 
33
	
YHR129C
1 
29
	
YLR376C
1 
19
	
YDR311W
1 
27
	
YDR206W
1 
12
	
YOL149W
1 
12
	
YER065C
1 
10
	
YNL218W
1 
24
	
YOR078W
1 
31
	
YPL019C
1 
42
	
YGL153W
1 
48
	
YDL002C
1 
 8

In [65]:

    

sapply(as.character(2:7), function(i) sapply(as.character(2:7), function(j) numSharedTerms(i, j)))


    

    






2
3
4
5
6
7

	
2
51
 0
 0
 0
 2
 2
	
3
 0
51
 1
 1
 1
 0
	
4
 0
 1
36
 1
 0
 1
	
5
 0
 1
 1
32
 0
 0
	
6
 2
 1
 0
 0
41
 0
	
7
 2
 0
 1
 0
 0
40

In [66]:

    

getShortestPath("7")


    

    






15
16

	
15
0
1
	
16
1
0

In [58]:

    

intersect(names(enrichmentResults[["p-values", "4"]]), names(enrichmentResults[["p-values", "2"]]))


    

In [59]:

    

intersect(names(enrichmentResults[["p-values", "4"]]), names(enrichmentResults[["p-values", "14"]]))


    

    






	
'GO:0015031'
	
'GO:0006999'
	
'GO:0001113'
	
'GO:0006913'
	
'GO:0046777'
	
'GO:0072417'
	
'GO:0032147'
	
'GO:0007118'
	
'GO:0051028'
	
'GO:0060188'
	
'GO:0030474'

In [60]:

    

intersect(names(enrichmentResults[["p-values", "4"]]), names(enrichmentResults[["p-values", "13"]]))


    

    






	
'GO:0032880'
	
'GO:0007032'
	
'GO:0036010'
	
'GO:0006810'
	
'GO:0015693'

In [61]:

    

intersect(names(enrichmentResults[["p-values", "13"]]), names(enrichmentResults[["p-values", "14"]]))


    

In [22]:

    

select(GO.db, keys=names(enrichmentResults[["p-values", 4]]), columns=c("GOID", "TERM", "DEFINITION"))


    

    




'select()' returned 1:1 mapping between keys and columns






    






GOID
TERM
DEFINITION

	
GO:0032258                                                                                                                                                                                                                                                                                                                                                                                                                                                               
CVT pathway                                                                                                                                                                                                                                                                                                                                                                                                                                                              
A constitutive biosynthetic process that occurs under nutrient-rich conditions, in which two resident vacuolar hydrolases, aminopeptidase I and alpha-mannosidase, are sequestered into vesicles; these vesicles are transported to, and then fuse with, the vacuole. This pathway is mostly observed in yeast.                                                                                                                                                          
	
GO:0000045                                                                                                                                                                                                                                                                                                                                                                                                                                                               
autophagosome assembly                                                                                                                                                                                                                                                                                                                                                                                                                                                   
The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.                                                                                                                                                                                                                                                                       
	
GO:0000422                                                                                                                                                                                                                                                                                                                                                                                                                                                               
mitophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.                                                                                                                                                                                                                                                                                                                                      
	
GO:0015031                                                                                                                                                                                                                                                                                                                                                                                                                                                               
protein transport                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                                 
	
GO:0032880                                                                                                                                                                                                                                                                                                                                                                                                                                                               
regulation of protein localization                                                                                                                                                                                                                                                                                                                                                                                                                                       
Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.                                                                                                                                                                                                                                                                                                                     
	
GO:0006606                                                                                                                                                                                                                                                                                                                                                                                                                                                               
protein import into nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                              
The directed movement of a protein from the cytoplasm to the nucleus.                                                                                                                                                                                                                                                                                                                                                                                                    
	
GO:0030242                                                                                                                                                                                                                                                                                                                                                                                                                                                               
pexophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The process in which peroxisomes are delivered to the vacuole and degraded in response to changing nutrient conditions.                                                                                                                                                                                                                                                                                                                                                  
	
GO:0007032                                                                                                                                                                                                                                                                                                                                                                                                                                                               
endosome organization                                                                                                                                                                                                                                                                                                                                                                                                                                                    
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.                                                                                                                                                                                                                                                                                                                        
	
GO:0007034                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuolar transport                                                                                                                                                                                                                                                                                                                                                                                                                                                       
The directed movement of substances into, out of or within a vacuole.                                                                                                                                                                                                                                                                                                                                                                                                    
	
GO:0007035                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuolar acidification                                                                                                                                                                                                                                                                                                                                                                                                                                                   
Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion.                                                                                                                                                                                                                                                                                                                                                                       
	
GO:0044206                                                                                                                                                                                                                                                                                                                                                                                                                                                               
UMP salvage                                                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.                                                                                                                                                                                                                                                                                                                              
	
GO:0044805                                                                                                                                                                                                                                                                                                                                                                                                                                                               
late nucleophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                         
A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.                                                                                                                                                                                                                                                              
	
GO:0006999                                                                                                                                                                                                                                                                                                                                                                                                                                                               
nuclear pore organization                                                                                                                                                                                                                                                                                                                                                                                                                                                
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.                                                                                                                                                                                                                                                                                                                 
	
GO:0034727                                                                                                                                                                                                                                                                                                                                                                                                                                                               
piecemeal microautophagy of nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                      
Degradation of a cell nucleus by lysosomal microautophagy.                                                                                                                                                                                                                                                                                                                                                                                                               
	
GO:0001113                                                                                                                                                                                                                                                                                                                                                                                                                                                               
transcriptional open complex formation at RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                     
Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.                                                                                                                                                    
	
GO:0070072                                                                                                                                                                                                                                                                                                                                                                                                                                                               
vacuolar proton-transporting V-type ATPase complex assembly                                                                                                                                                                                                                                                                                                                                                                                                              
The aggregation, arrangement and bonding together of a vacuolar proton-transporting V-type ATPase complex, proton-transporting two-sector ATPase complex that couples ATP hydrolysis to the transport of protons across the vacuolar membrane.                                                                                                                                                                                                                           
	
GO:0051301                                                                                                                                                                                                                                                                                                                                                                                                                                                               
cell division                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.                                                                                                                                                                                                                                           
	
GO:0006913                                                                                                                                                                                                                                                                                                                                                                                                                                                               
nucleocytoplasmic transport                                                                                                                                                                                                                                                                                                                                                                                                                                              
The directed movement of molecules between the nucleus and the cytoplasm.                                                                                                                                                                                                                                                                                                                                                                                                
	
GO:0006914                                                                                                                                                                                                                                                                                                                                                                                                                                                               
autophagy                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.                                                                                                                                                                                                                                        
	
GO:0046777                                                                                                                                                                                                                                                                                                                                                                                                                                                               
protein autophosphorylation                                                                                                                                                                                                                                                                                                                                                                                                                                              
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).                                                                                                                                                                                                                                                                                               
	
GO:0072417                                                                                                                                                                                                                                                                                                                                                                                                                                                               
response to spindle checkpoint signaling                                                                                                                                                                                                                                                                                                                                                                                                                                 
A process that occurs in response to signals generated as a result of spindle checkpoint signaling.                                                                                                                                                                                                                                                                                                                                                                      
	
GO:0006890                                                                                                                                                                                                                                                                                                                                                                                                                                                               
retrograde vesicle-mediated transport, Golgi to ER                                                                                                                                                                                                                                                                                                                                                                                                                       
The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.                                                                                                                                                                                                                                                                                                           
	
GO:0045048                                                                                                                                                                                                                                                                                                                                                                                                                                                               
protein insertion into ER membrane                                                                                                                                                                                                                                                                                                                                                                                                                                       
The process that results in incorporation of a protein into an endoplasmic reticulum (ER) membrane. It depends on specific topogenic sequences of amino acids that ensure that a protein acquires the proper orientation during its insertion into the ER membrane.                                                                                                                                                                                                      
	
GO:0032147                                                                                                                                                                                                                                                                                                                                                                                                                                                               
activation of protein kinase activity                                                                                                                                                                                                                                                                                                                                                                                                                                    
Any process that initiates the activity of an inactive protein kinase.                                                                                                                                                                                                                                                                                                                                                                                                   
	
GO:0007118                                                                                                                                                                                                                                                                                                                                                                                                                                                               
budding cell apical bud growth                                                                                                                                                                                                                                                                                                                                                                                                                                           
Growth at the tip of a bud, in a cell that reproduces by budding.                                                                                                                                                                                                                                                                                                                                                                                                        
	
GO:0048213                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Golgi vesicle prefusion complex stabilization                                                                                                                                                                                                                                                                                                                                                                                                                            
The binding of specific proteins to the t-SNARE/v-SNARE/SNAP25 complex, by which the Golgi vesicle prefusion complex is stabilized.                                                                                                                                                                                                                                                                                                                                      
	
GO:0051028                                                                                                                                                                                                                                                                                                                                                                                                                                                               
mRNA transport                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                        
	
GO:0000301                                                                                                                                                                                                                                                                                                                                                                                                                                                               
retrograde transport, vesicle recycling within Golgi                                                                                                                                                                                                                                                                                                                                                                                                                     
The retrograde movement of substances within the Golgi, mediated by COP I vesicles. Cis-Golgi vesicles are constantly moving forward through the Golgi stack by cisternal progression, eventually becoming trans-Golgi vesicles. They then selectively transport membrane and luminal proteins from the trans- to the medial-Golgi while leaving others behind in the trans-Golgi cisternae; similarly, they selectively move proteins from the medial- to the cis-Golgi.
	
GO:0036010                                                                                                                                                                                                                                                                                                                                                                                                                                                               
protein localization to endosome                                                                                                                                                                                                                                                                                                                                                                                                                                         
A process in which a protein is transported to, or maintained in, a location within an endosome.                                                                                                                                                                                                                                                                                                                                                                         
	
GO:0060188                                                                                                                                                                                                                                                                                                                                                                                                                                                               
regulation of protein desumoylation                                                                                                                                                                                                                                                                                                                                                                                                                                      
Any process that modulates the frequency, rate or extent of protein desumoylation. Protein desumoylation is the process in which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.                                                                                                                                                                                                                                                   
	
GO:0016560                                                                                                                                                                                                                                                                                                                                                                                                                                                               
protein import into peroxisome matrix, docking                                                                                                                                                                                                                                                                                                                                                                                                                           
The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.                                                                                                                                                                                                                                                                                   
	
GO:0000055                                                                                                                                                                                                                                                                                                                                                                                                                                                               
ribosomal large subunit export from nucleus                                                                                                                                                                                                                                                                                                                                                                                                                              
The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.                                                                                                                                                                                                                                                                                                                                                                                  
	
GO:0006810                                                                                                                                                                                                                                                                                                                                                                                                                                                               
transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.                                                                                                                                                                   
	
GO:0015693                                                                                                                                                                                                                                                                                                                                                                                                                                                               
magnesium ion transport                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The directed movement of magnesium (Mg) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                      
	
GO:0030474                                                                                                                                                                                                                                                                                                                                                                                                                                                               
spindle pole body duplication                                                                                                                                                                                                                                                                                                                                                                                                                                            
Construction of a new spindle pole body.                                                                                                                                                                                                                                                                                                                                                                                                                                 
	
GO:0016973                                                                                                                                                                                                                                                                                                                                                                                                                                                               
poly(A)+ mRNA export from nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                        
The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.                                                                                                                                                                                                                                                                                                                                                                                            

In [25]:

    

select(GO.db, keys=names(enrichmentResults[["p-values", 14]]), columns=c("GOID", "TERM", "DEFINITION"))


    

    




'select()' returned 1:1 mapping between keys and columns






    






GOID
TERM
DEFINITION

	
GO:0046777                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
protein autophosphorylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
	
GO:0006913                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
nucleocytoplasmic transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
The directed movement of molecules between the nucleus and the cytoplasm.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
	
GO:0000920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
cell separation after cytokinesis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
	
GO:0001113                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
transcriptional open complex formation at RNA polymerase II promoter                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.                                                                                                                                                                                                                                                                                                                                                                                              
	
GO:0006607                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
NLS-bearing protein import into nucleus                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
	
GO:0042981                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
regulation of apoptotic process                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
Any process that modulates the occurrence or rate of cell death by apoptotic process.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
	
GO:0070816                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
phosphorylation of RNA polymerase II C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex.
	
GO:0031990                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
mRNA export from nucleus in response to heat stress                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
The directed movement of mRNA from the nucleus to the cytoplasm during a heat stimulus, a temperature stimulus above the optimal temperature for the organism; in particular, a process that enables an organism withstand exposure to temperatures that would otherwise lethally impair poly(A)+ mRNA-nucleus export.                                                                                                                                                                                                                                                                                                                                                                                             
	
GO:0031098                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
stress-activated protein kinase signaling cascade                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
A series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays one or more of the signals.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
	
GO:0007039                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
protein catabolic process in the vacuole                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
GO:0015031                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
protein transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
GO:0051028                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
mRNA transport                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
GO:0034501                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
protein localization to kinetochore                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
Any process in which a protein is transported to, or maintained at, the kinetochore.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
	
GO:0030474                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
spindle pole body duplication                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
Construction of a new spindle pole body.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
GO:0060188                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
regulation of protein desumoylation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
Any process that modulates the frequency, rate or extent of protein desumoylation. Protein desumoylation is the process in which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
GO:0006999                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
nuclear pore organization                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
	
GO:0032147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
activation of protein kinase activity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
Any process that initiates the activity of an inactive protein kinase.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
	
GO:0007118                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
budding cell apical bud growth                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Growth at the tip of a bud, in a cell that reproduces by budding.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
	
GO:0072417                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
response to spindle checkpoint signaling                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
A process that occurs in response to signals generated as a result of spindle checkpoint signaling.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                

In [23]:

    

getSubCommunities(4)


    

    






	
'14'
	
'10'
	
'12'
	
'11'
	
'13'

In [20]:

    

layerMeanMapSimilarities


    

    






	
0
		
0.641066666666667
	
1
		
0.461577777777778
	
2
		
0.365219367588933

In [ ]:

    

getDistance <- function(c1, c2) {
    
    m1 <- getSuperCommunity(c1)
    m2 <- getSuperCommunity(c2)
    
    if (m1 == m2) return(getShortestPath(m1)[c1, c2])
        
    d1 <- getDepth(c1)
    d2 <- getDepth(c2)
        
    if (d1 == d2) return (2 + getDistance(m1, m2))
        
    if (d1 > d2) return (1 + getDistance(m1, c2))
        
    if (d2 > d1) return (1 + getDistance(c1, m2))
    
}


    

In [78]:

    

distances <- sapply(as.character(2:max(assignments)), function(i)
    sapply(as.character(2:max(assignments)), function(j) {
        return(getDistance(i, j))
    }))


    

    




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[1] "attempting 53 2"
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[1] "attempting 53 11"
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[1] "attempting 53 15"
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[1] "attempting 53 18"
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[1] "attempting 53 21"
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[1] "attempting 53 27"
[1] "attempting 53 28"
[1] "attempting 53 29"
[1] "attempting 53 30"
[1] "attempting 53 31"
[1] "attempting 53 32"
[1] "attempting 53 33"
[1] "attempting 53 34"
[1] "attempting 53 35"
[1] "attempting 53 36"
[1] "attempting 53 37"
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[1] "attempting 53 39"
[1] "attempting 53 40"
[1] "attempting 53 41"
[1] "attempting 53 42"
[1] "attempting 53 43"
[1] "attempting 53 44"
[1] "attempting 53 45"
[1] "attempting 53 46"
[1] "attempting 53 47"
[1] "attempting 53 48"
[1] "attempting 53 49"
[1] "attempting 53 50"
[1] "attempting 53 51"
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[1] "attempting 53 53"
[1] "attempting 53 54"
[1] "attempting 53 55"
[1] "attempting 53 56"
[1] "attempting 53 57"
[1] "attempting 53 58"
[1] "attempting 54 2"
[1] "attempting 54 3"
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[1] "attempting 54 11"
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[1] "attempting 54 18"
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[1] "attempting 54 20"
[1] "attempting 54 21"
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[1] "attempting 54 27"
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[1] "attempting 54 29"
[1] "attempting 54 30"
[1] "attempting 54 31"
[1] "attempting 54 32"
[1] "attempting 54 33"
[1] "attempting 54 34"
[1] "attempting 54 35"
[1] "attempting 54 36"
[1] "attempting 54 37"
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[1] "attempting 54 40"
[1] "attempting 54 41"
[1] "attempting 54 42"
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[1] "attempting 54 45"
[1] "attempting 54 46"
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[1] "attempting 54 48"
[1] "attempting 54 49"
[1] "attempting 54 50"
[1] "attempting 54 51"
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[1] "attempting 54 53"
[1] "attempting 54 54"
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[1] "attempting 54 58"
[1] "attempting 55 2"
[1] "attempting 55 3"
[1] "attempting 55 4"
[1] "attempting 55 5"
[1] "attempting 55 6"
[1] "attempting 55 7"
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[1] "attempting 55 9"
[1] "attempting 55 10"
[1] "attempting 55 11"
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[1] "attempting 55 20"
[1] "attempting 55 21"
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[1] "attempting 55 24"
[1] "attempting 55 25"
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[1] "attempting 55 27"
[1] "attempting 55 28"
[1] "attempting 55 29"
[1] "attempting 55 30"
[1] "attempting 55 31"
[1] "attempting 55 32"
[1] "attempting 55 33"
[1] "attempting 55 34"
[1] "attempting 55 35"
[1] "attempting 55 36"
[1] "attempting 55 37"
[1] "attempting 55 38"
[1] "attempting 55 39"
[1] "attempting 55 40"
[1] "attempting 55 41"
[1] "attempting 55 42"
[1] "attempting 55 43"
[1] "attempting 55 44"
[1] "attempting 55 45"
[1] "attempting 55 46"
[1] "attempting 55 47"
[1] "attempting 55 48"
[1] "attempting 55 49"
[1] "attempting 55 50"
[1] "attempting 55 51"
[1] "attempting 55 52"
[1] "attempting 55 53"
[1] "attempting 55 54"
[1] "attempting 55 55"
[1] "attempting 55 56"
[1] "attempting 55 57"
[1] "attempting 55 58"
[1] "attempting 56 2"
[1] "attempting 56 3"
[1] "attempting 56 4"
[1] "attempting 56 5"
[1] "attempting 56 6"
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[1] "attempting 56 8"
[1] "attempting 56 9"
[1] "attempting 56 10"
[1] "attempting 56 11"
[1] "attempting 56 12"
[1] "attempting 56 13"
[1] "attempting 56 14"
[1] "attempting 56 15"
[1] "attempting 56 16"
[1] "attempting 56 17"
[1] "attempting 56 18"
[1] "attempting 56 19"
[1] "attempting 56 20"
[1] "attempting 56 21"
[1] "attempting 56 22"
[1] "attempting 56 23"
[1] "attempting 56 24"
[1] "attempting 56 25"
[1] "attempting 56 26"
[1] "attempting 56 27"
[1] "attempting 56 28"
[1] "attempting 56 29"
[1] "attempting 56 30"
[1] "attempting 56 31"
[1] "attempting 56 32"
[1] "attempting 56 33"
[1] "attempting 56 34"
[1] "attempting 56 35"
[1] "attempting 56 36"
[1] "attempting 56 37"
[1] "attempting 56 38"
[1] "attempting 56 39"
[1] "attempting 56 40"
[1] "attempting 56 41"
[1] "attempting 56 42"
[1] "attempting 56 43"
[1] "attempting 56 44"
[1] "attempting 56 45"
[1] "attempting 56 46"
[1] "attempting 56 47"
[1] "attempting 56 48"
[1] "attempting 56 49"
[1] "attempting 56 50"
[1] "attempting 56 51"
[1] "attempting 56 52"
[1] "attempting 56 53"
[1] "attempting 56 54"
[1] "attempting 56 55"
[1] "attempting 56 56"
[1] "attempting 56 57"
[1] "attempting 56 58"
[1] "attempting 57 2"
[1] "attempting 57 3"
[1] "attempting 57 4"
[1] "attempting 57 5"
[1] "attempting 57 6"
[1] "attempting 57 7"
[1] "attempting 57 8"
[1] "attempting 57 9"
[1] "attempting 57 10"
[1] "attempting 57 11"
[1] "attempting 57 12"
[1] "attempting 57 13"
[1] "attempting 57 14"
[1] "attempting 57 15"
[1] "attempting 57 16"
[1] "attempting 57 17"
[1] "attempting 57 18"
[1] "attempting 57 19"
[1] "attempting 57 20"
[1] "attempting 57 21"
[1] "attempting 57 22"
[1] "attempting 57 23"
[1] "attempting 57 24"
[1] "attempting 57 25"
[1] "attempting 57 26"
[1] "attempting 57 27"
[1] "attempting 57 28"
[1] "attempting 57 29"
[1] "attempting 57 30"
[1] "attempting 57 31"
[1] "attempting 57 32"
[1] "attempting 57 33"
[1] "attempting 57 34"
[1] "attempting 57 35"
[1] "attempting 57 36"
[1] "attempting 57 37"
[1] "attempting 57 38"
[1] "attempting 57 39"
[1] "attempting 57 40"
[1] "attempting 57 41"
[1] "attempting 57 42"
[1] "attempting 57 43"
[1] "attempting 57 44"
[1] "attempting 57 45"
[1] "attempting 57 46"
[1] "attempting 57 47"
[1] "attempting 57 48"
[1] "attempting 57 49"
[1] "attempting 57 50"
[1] "attempting 57 51"
[1] "attempting 57 52"
[1] "attempting 57 53"
[1] "attempting 57 54"
[1] "attempting 57 55"
[1] "attempting 57 56"
[1] "attempting 57 57"
[1] "attempting 57 58"
[1] "attempting 58 2"
[1] "attempting 58 3"
[1] "attempting 58 4"
[1] "attempting 58 5"
[1] "attempting 58 6"
[1] "attempting 58 7"
[1] "attempting 58 8"
[1] "attempting 58 9"
[1] "attempting 58 10"
[1] "attempting 58 11"
[1] "attempting 58 12"
[1] "attempting 58 13"
[1] "attempting 58 14"
[1] "attempting 58 15"
[1] "attempting 58 16"
[1] "attempting 58 17"
[1] "attempting 58 18"
[1] "attempting 58 19"
[1] "attempting 58 20"
[1] "attempting 58 21"
[1] "attempting 58 22"
[1] "attempting 58 23"
[1] "attempting 58 24"
[1] "attempting 58 25"
[1] "attempting 58 26"
[1] "attempting 58 27"
[1] "attempting 58 28"
[1] "attempting 58 29"
[1] "attempting 58 30"
[1] "attempting 58 31"
[1] "attempting 58 32"
[1] "attempting 58 33"
[1] "attempting 58 34"
[1] "attempting 58 35"
[1] "attempting 58 36"
[1] "attempting 58 37"
[1] "attempting 58 38"
[1] "attempting 58 39"
[1] "attempting 58 40"
[1] "attempting 58 41"
[1] "attempting 58 42"
[1] "attempting 58 43"
[1] "attempting 58 44"
[1] "attempting 58 45"
[1] "attempting 58 46"
[1] "attempting 58 47"
[1] "attempting 58 48"
[1] "attempting 58 49"
[1] "attempting 58 50"
[1] "attempting 58 51"
[1] "attempting 58 52"
[1] "attempting 58 53"
[1] "attempting 58 54"
[1] "attempting 58 55"
[1] "attempting 58 56"
[1] "attempting 58 57"
[1] "attempting 58 58"

In [80]:

    

head(distances)


    

    






2
3
4
5
6
7
8
9
10
11
⋯
49
50
51
52
53
54
55
56
57
58

	
2
0
1
1
2
2
1
3
2
2
3
⋯
4
3
3
3
3
3
3
5
5
5
	
3
1
0
1
1
1
1
2
1
1
2
⋯
3
3
3
3
3
3
3
4
4
4
	
4
1
1
0
1
2
2
2
2
2
3
⋯
4
4
4
4
4
4
4
5
5
5
	
5
2
1
1
0
1
2
1
2
2
3
⋯
3
4
4
4
4
4
4
4
4
4
	
6
2
1
2
1
0
2
1
1
2
2
⋯
2
4
4
4
4
4
4
3
3
3
	
7
1
1
2
2
2
0
3
2
2
3
⋯
4
2
2
2
2
2
2
5
5
5

In [84]:

    

similarities <- sapply(2:max(assignments), function(i)
    sapply(2:max(assignments), function(j) {
        return(clusterSim(cluster1 = geneCommunities[[i]], 
                          cluster2 = geneCommunities[[j]], semData = scGO, measure = "Wang", combine = "BMA"))
    }))


    

In [86]:

    

head(similarities)


    

    







	
1.000
0.336
0.661
0.620
0.617
0.662
0.578
0.551
0.626
0.418
⋯    
0.443
0.177
0.528
0.286
0.418
0.319
0.212
0.436
0.270
0.420
	
0.336
1.000
0.318
0.355
0.314
0.324
0.303
0.323
0.433
0.389
⋯    
0.339
0.234
0.276
0.375
0.394
0.296
0.178
0.285
0.252
0.221
	
0.661
0.318
1.000
0.627
0.675
0.639
0.639
0.485
0.594
0.398
⋯    
0.477
0.170
0.508
0.350
0.444
0.303
0.238
0.467
0.242
0.421
	
0.620
0.355
0.627
1.000
0.626
0.630
0.604
0.452
0.557
0.412
⋯    
0.408
0.198
0.501
0.323
0.432
0.350
0.222
0.432
0.238
0.361
	
0.617
0.314
0.675
0.626
1.000
0.640
0.653
0.499
0.593
0.469
⋯    
0.528
0.184
0.493
0.325
0.433
0.318
0.212
0.561
0.358
1.000
	
0.662
0.324
0.639
0.630
0.640
1.000
0.586
0.424
0.588
0.451
⋯    
0.439
0.189
0.597
0.305
0.455
0.359
0.269
0.423
0.265
0.388

In [14]:

    

uniprots <- sapply(1:max(assignments), function(i) {
    orfs <- getGenes(i)
    orfs <- orfs[orfs %in% allGenesInDB]
    return(as.character(org.Sc.sgdUNIPROT[orfs]))
})


    

    




Warning message in .local(x, ...):
“returned vector has duplicated names”Warning message in .local(x, ...):
“returned vector has duplicated names”Warning message in .local(x, ...):
“returned vector has duplicated names”Warning message in .local(x, ...):
“returned vector has duplicated names”

In [15]:

    

uniprots[1]


    

    






	

	
YAL032C
		
'P28004'
	
YAL040C
		
'P13365'
	
YBL007C
		
'P32790'
	
YBR057C
		
'P38236'
	
YBR094W
		
'P38254'
	
YBR133C
		
'P38274'
	
YBR196C
		
'P12709'
	
YBR221C
		
'P32473'
	
YBR252W
		
'P33317'
	
YBR270C
		
'P38346'
	
YBR274W
		
'P38147'
	
YCL054W
		
'P25582'
	
YCL055W
		
'P25583'
	
YCR011C
		
'P25371'
	
YCR050C
		
'P25630'
	
YCR086W
		
'P25651'
	
YDL002C
		
'Q03435'
	
YDL012C
		
'Q12489'
	
YDL013W
		
'P32828'
	
YDL017W
		
'P06243'
	
YDL088C
		
'Q05166'
	
YDL110C
		
'Q12513'
	
YDL111C
		
'Q12277'
	
YDL154W
		
'Q12175'
	
YDL160C
		
'P39517'
	
YDL165W
		
'P06100'
	
YDL203C
		
'Q07622'
	
YDL215C
		
'P33327'
	
YDL236W
		
'P19881'
	
YDL246C
		
'Q07786'
	
YDR054C
		
'P14682'
	
YDR061W
		
'Q12298'
	
YDR078C
		
'P38957'
	
YDR106W
		
'Q04549'
	
YDR122W
		
'P13185'
	
YDR148C
		
'P19262'
	
YDR151C
		
'P47976'
	
YDR167W
		
'Q12030'
	
YDR174W
		
'Q03973'
	
YDR201W
		
'Q03954'
	
YDR206W
		
'Q03466'
	
YDR207C
		
'P39001'
	
YDR214W
		
'Q12449'
	
YDR273W
		
'Q05610'
	
YDR311W
		
'P32776'
	
YDR315C
		
'Q06667'
	
YDR326C
		
'Q06681'
	
YDR383C
		
'Q12493'
	
YDR439W
		
'Q04087'
	
YDR469W
		
'Q03323'
	
YDR477W
		
'P06782'
	
YDR503C
		
'Q04396'
	
YDR510W
		
'Q12306'
	
YEL015W
		
'P39998'
	
YEL023C
		
'P39992'
	
YEL062W
		
'P39923'
	
YER027C
		
'Q04739'
	
YER065C
		
'P28240'
	
YER079W
		
'P40052'
	
YER092W
		
'P40060'
	
YER105C
		
'P40064'
	
YER116C
		
'P40072'
	
YER179W
		
'P25453'
	
YFL061W
		
'P0CH63'
	
YFL061W
		
'P0CH64'
	
YFR002W
		
'P34077'
	
YFR033C
		
'P00127'
	
YFR047C
		
'P43619'
	
YFR052W
		
'P32496'
	
YFR057W
		
'P43625'
	
YGL025C
		
'P40356'
	
YGL112C
		
'P53040'
	
YGL115W
		
'P12904'
	
YGL116W
		
'P26309'
	
YGL122C
		
'P32505'
	
YGL145W
		
'P33891'
	
YGL150C
		
'P53115'
	
YGL153W
		
'P53112'
	
YGL158W
		
'P38622'
	
YGL170C
		
'P45819'
	
YGL172W
		
'Q02199'
	
YGL175C
		
'P46946'
	
YGL180W
		
'P53104'
	
YGL192W
		
'P41833'
	
YGL208W
		
'P34164'
	
YGL221C
		
'P53081'
	
YGL229C
		
'P53036'
	
YGL238W
		
'P33307'
	
YGR014W
		
'P32334'
	
YGR024C
		
'P53215'
	
YGR046W
		
'P53230'
	
YGR057C
		
'P53237'
	
YGR058W
		
'P53238'
	
YGR099W
		
'P53038'
	
YGR117C
		
'P53270'
	
YGR119C
		
'P48837'
	
YGR120C
		
'P53271'
	
YGR136W
		
'P53281'
	
YGR155W
		
'P32582'
	
YGR158C
		
'P48240'
	
YGR253C
		
'P32379'
	
YGR268C
		
'P40325'
	
YHL006C
		
'P38751'
	
YHL009C
		
'P38749'
	
YHL046C
		
'P38725'
	
YHR016C
		
'P32793'
	
YHR032W
		
'P38767'
	
YHR057C
		
'P23285'
	
YHR060W
		
'P38784'
	
YHR102W
		
'P38692'
	
YHR128W
		
'P18562'
	
YHR129C
		
'P38696'
	
YHR140W
		
'P38842'
	
YHR158C
		
'P38853'
	
YIL013C
		
'P40550'
	
YIL065C
		
'P40515'
	
YIL105C
		
'P40485'
	
YIL132C
		
'P40465'
	
YIL144W
		
'P40460'
	
YIL172C
		
'P0CW40'
	
YIL172C
		
'P0CW41'
	
YJL013C
		
'P47074'
	
YJL030W
		
'P40958'
	
YJL041W
		
'P14907'
	
YJL048C
		
'P47049'
	
YJL057C
		
'P47042'
	
YJL065C
		
'P40366'
	
YJL088W
		
'P05150'
	
YJL092W
		
'P12954'
	
YJL110C
		
'P42944'
	
YJL178C
		
'P46989'
	
YJL184W
		
'P46984'
	
YJR034W
		
'Q02772'
	
YJR072C
		
'P47122'
	
YJR091C
		
'P47135'
	
YJR117W
		
'P47154'
	
YJR122W
		
'P47158'
	
YJR133W
		
'P47165'
	
YJR159W
		
'P35497'
	
YKL012W
		
'P33203'
	
YKL015W
		
'P25502'
	
YKL028W
		
'P36100'
	
YKL039W
		
'P32857'
	
YKL061W
		
'P35727'
	
YKL075C
		
'P36083'
	
YKL090W
		
'P36075'
	
YKL103C
		
'P14904'
	
YKL130C
		
'P36068'
	
YKL204W
		
'P36041'
	
YKR026C
		
'P14741'
	
YKR037C
		
'P36131'
	
YKR062W
		
'P36145'
	
YLL046C
		
'P32385'
	
YLR015W
		
'P43132'
	
YLR046C
		
'Q12253'
	
YLR113W
		
'P32485'
	
YLR150W
		
'P39015'
	
YLR243W
		
'Q06543'
	
YLR258W
		
'P27472'
	
YLR264W
		
'P0C0X0'
	
YLR291C
		
'P32502'
	
YLR303W
		
'P06106'
	
YLR305C
		
'P37297'
	
YLR315W
		
'Q06162'
	
YLR321C
		
'Q06168'
	
YLR323C
		
'P53769'
	
YLR345W
		
'Q06137'
	
YLR376C
		
'Q12318'
	
YLR392C
		
'P18634'
	
YLR423C
		
'Q06410'
	
YLR432W
		
'P50095'
	
YLR433C
		
'P23287'
	
YLR447C
		
'P32366'
	
YML015C
		
'Q04226'
	
YML028W
		
'P34760'
	
YML031W
		
'P32500'
	
YML114C
		
'Q03750'
	
YMR068W
		
'Q04749'
	
YMR102C
		
'Q03177'
	
YMR129W
		
'P39685'
	
YMR153W
		
'Q03790'
	
YMR180C
		
'Q03220'
	
YMR181C
		
'Q03231'
	
YMR224C
		
'P32829'
	
YMR226C
		
'Q05016'
	
YMR236W
		
'Q05027'
	
YMR255W
		
'Q04839'
	
YMR267W
		
'P28239'
	
YMR269W
		
'Q03525'
	
YMR309C
		
'P32497'
	
YMR314W
		
'P40302'
	
YNL021W
		
'P53973'
	
YNL023C
		
'P53971'
	
YNL047C
		
'P53955'
	
YNL086W
		
'P48232'
	
YNL091W
		
'P53935'
	
YNL118C
		
'P53550'
	
YNL122C
		
'P53921'
	
YNL154C
		
'P23292'
	
YNL164C
		
'P53892'
	
YNL189W
		
'Q02821'
	
YNL199C
		
'Q01722'
	
YNL201C
		
'P40164'
	
YNL218W
		
'P40151'
	
YNL236W
		
'P32259'
	
YNL244C
		
'P32911'
	
YNL288W
		
'P53829'
	
YNR029C
		
'P53729'
	
YNR048W
		
'P53740'
	
YOL020W
		
'P38967'
	
YOL058W
		
'P22768'
	
YOL082W
		
'P35193'
	
YOL105C
		
'Q12215'
	
YOL123W
		
'Q99383'
	
YOL130W
		
'Q08269'
	
YOL149W
		
'Q12517'
	
YOR006C
		
'Q12094'
	
YOR026W
		
'P26449'
	
YOR036W
		
'P32854'
	
YOR047C
		
'Q02794'
	
YOR062C
		
'P36025'
	
YOR078W
		
'Q08492'
	
YOR115C
		
'Q99394'
	
YOR138C
		
'Q12242'
	
YOR164C
		
'Q12125'
	
YOR262W
		
'Q08726'
	
YOR264W
		
'Q08729'
	
YOR284W
		
'Q12134'
	
YOR353C
		
'Q08817'
	
YOR355W
		
'P41913'
	
YOR372C
		
'Q08887'
	
YPL019C
		
'Q02725'
	
YPL059W
		
'Q02784'
	
YPL070W
		
'Q02866'
	
YPL110C
		
'Q02979'
	
YPL111W
		
'P00812'
	
YPL128C
		
'Q02457'
	
YPL151C
		
'Q12417'
	
YPL174C
		
'P33420'
	
YPL211W
		
'Q08962'
	
YPL214C
		
'P41835'
	
YPL229W
		
'Q99395'
	
YPL260W
		
'Q08977'
	
YPR020W
		
'Q12233'
	
YPR040W
		
'Q12199'
	
YPR048W
		
'Q12181'
	
YPR062W
		
'Q12178'
	
YPR070W
		
'Q12321'
	
YPR105C
		
'Q06096'
	
YPR115W
		
'Q06108'
	
YPR185W
		
'Q06628'

In [12]:

    

g <- getGenes(2)[getGenes(2) %in% allGenesInDB]


    

In [13]:

    

org.Sc.sgdUNIPROT[g]


    

    






UNIPROT submap for Yeast (object of class "AnnDbBimap")

In [ ]: