In [1]:

    

#libraries
library(GO.db)
library(topGO)
# library(org.Hs.eg.db)
library(org.Sc.sgd.db)
library(GOSemSim)


    

    




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

In [2]:

    

file <- "yeast_uetz"

ont <- "BP"
p <- 0.8
init <- 1

db <- org.Sc.sgd.db
mapping <- "org.Sc.sgd.db"
ID <- "ENSEMBL"
# db <- org.Hs.eg.db
# mapping <- "org.Hs.eg.db"
# ID <- "ENTREZ"

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

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

#load communities from file
g <- list()
numCom <- 0
filename <- sprintf("community_%s.txt", numCom)
while (file.exists(filename)) {
    numCom <- numCom + 1
    g[[numCom]] <- scan(filename, character())
    filename <- sprintf("community_%s.txt", numCom)
}

#distances between neurons
shortest.path <- read.csv("shortest_path.csv", sep=",", header=FALSE)


    

In [3]:

    

numCom


    

    





6

In [4]:

    

##SEMATIC SIMILARITY
#construct gosemsim object

scGO <- godata(mapping, ont=ont, keytype=ID)
print("DONE")


    

    




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

In [64]:

    

allGeneNames <- scan(character(), file="../yeast_uetz_communities_0.5_1/all_genes.txt")

g  <- sapply(g, function(i) allGeneNames[as.integer(i)])
allGenes <- allGeneNames[as.integer(allGenes)]


    

In [5]:

    

interestingGenes <- factor(as.integer(allGenes %in% g[[1]]))
names(interestingGenes) <- allGenes

GOdata <- new("topGOdata", description=sprintf("topGO object"),
          ontology = ont, allGenes = interestingGenes,
          annotationFun = annFUN.org, mapping = mapping, 
          ID = ID, nodeSize = 10)


    

    




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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

In [9]:

    

usedGO(GOdata)


    

    






	
'GO:0000003'
	
'GO:0000070'
	
'GO:0000075'
	
'GO:0000278'
	
'GO:0000280'
	
'GO:0000288'
	
'GO:0000723'
	
'GO:0000819'
	
'GO:0000956'
	
'GO:0005975'
	
'GO:0006082'
	
'GO:0006091'
	
'GO:0006139'
	
'GO:0006259'
	
'GO:0006281'
	
'GO:0006302'
	
'GO:0006310'
	
'GO:0006325'
	
'GO:0006351'
	
'GO:0006352'
	
'GO:0006355'
	
'GO:0006357'
	
'GO:0006366'
	
'GO:0006367'
	
'GO:0006396'
	
'GO:0006397'
	
'GO:0006401'
	
'GO:0006402'
	
'GO:0006403'
	
'GO:0006412'
	
'GO:0006417'
	
'GO:0006461'
	
'GO:0006464'
	
'GO:0006468'
	
'GO:0006508'
	
'GO:0006518'
	
'GO:0006520'
	
'GO:0006605'
	
'GO:0006606'
	
'GO:0006725'
	
'GO:0006753'
	
'GO:0006793'
	
'GO:0006796'
	
'GO:0006807'
	
'GO:0006810'
	
'GO:0006886'
	
'GO:0006913'
	
'GO:0006914'
	
'GO:0006950'
	
'GO:0006974'
	
'GO:0006996'
	
'GO:0006997'
	
'GO:0007010'
	
'GO:0007033'
	
'GO:0007034'
	
'GO:0007049'
	
'GO:0007059'
	
'GO:0007067'
	
'GO:0007126'
	
'GO:0007154'
	
'GO:0007165'
	
'GO:0007346'
	
'GO:0008104'
	
'GO:0008150'
	
'GO:0008152'
	
'GO:0009056'
	
'GO:0009057'
	
'GO:0009058'
	
'GO:0009059'
	
'GO:0009116'
	
'GO:0009117'
	
'GO:0009123'
	
'GO:0009161'
	
'GO:0009259'
	
'GO:0009628'
	
'GO:0009653'
	
'GO:0009889'
	
'GO:0009890'
	
'GO:0009891'
	
'GO:0009892'
	
'GO:0009893'
	
'GO:0009987'
	
'GO:0010033'
	
'GO:0010467'
	
'GO:0010468'
	
'GO:0010556'
	
'GO:0010557'
	
'GO:0010558'
	
'GO:0010564'
	
'GO:0010604'
	
'GO:0010605'
	
'GO:0010608'
	
'GO:0010628'
	
'GO:0010629'
	
'GO:0010639'
	
'GO:0015031'
	
'GO:0015931'
	
'GO:0016043'
	
'GO:0016070'
	
'GO:0016071'
	
'GO:0016192'
	
'GO:0016236'
	
'GO:0016310'
	
'GO:0016569'
	
'GO:0017038'
	
'GO:0018130'
	
'GO:0018193'
	
'GO:0019219'
	
'GO:0019222'
	
'GO:0019438'
	
'GO:0019439'
	
'GO:0019538'
	
'GO:0019637'
	
'GO:0019693'
	
'GO:0019752'
	
'GO:0022402'
	
'GO:0022414'
	
'GO:0022607'
	
'GO:0022613'
	
'GO:0023052'
	
'GO:0030154'
	
'GO:0030163'
	
'GO:0031323'
	
'GO:0031324'
	
'GO:0031325'
	
'GO:0031326'
	
'GO:0031327'
	
'GO:0031328'
	
'GO:0032200'
	
'GO:0032268'
	
'GO:0032502'
	
'GO:0032774'
	
'GO:0033036'
	
'GO:0033043'
	
'GO:0033365'
	
'GO:0033554'
	
'GO:0034248'
	
'GO:0034504'
	
'GO:0034613'
	
'GO:0034622'
	
'GO:0034641'
	
'GO:0034645'
	
'GO:0034654'
	
'GO:0034655'
	
'GO:0034660'
	
'GO:0035556'
	
'GO:0036211'
	
'GO:0040007'
	
'GO:0042221'
	
'GO:0042254'
	
'GO:0042592'
	
'GO:0043043'
	
'GO:0043170'
	
'GO:0043412'
	
'GO:0043436'
	
'GO:0043603'
	
'GO:0043604'
	
'GO:0043623'
	
'GO:0043632'
	
'GO:0043933'
	
'GO:0044085'
	
'GO:0044087'
	
'GO:0044237'
	
'GO:0044238'
	
'GO:0044248'
	
'GO:0044249'
	
'GO:0044257'
	
'GO:0044260'
	
'GO:0044265'
	
'GO:0044267'
	
'GO:0044270'
	
'GO:0044271'
	
'GO:0044281'
	
'GO:0044283'
	
'GO:0044699'
	
'GO:0044700'
	
'GO:0044702'
	
'GO:0044710'
	
'GO:0044711'
	
'GO:0044712'
	
'GO:0044723'
	
'GO:0044744'
	
'GO:0044763'
	
'GO:0044765'
	
'GO:0044767'
	
'GO:0044770'
	
'GO:0044772'
	
'GO:0044802'
	
'GO:0045184'
	
'GO:0045786'
	
'GO:0045892'
	
'GO:0045893'
	
'GO:0045934'
	
'GO:0045935'
	
'GO:0045944'
	
'GO:0046483'
	
'GO:0046700'
	
'GO:0046907'
	
'GO:0048285'
	
'GO:0048518'
	
'GO:0048519'
	
'GO:0048522'
	
'GO:0048523'
	
'GO:0048583'
	
'GO:0048856'
	
'GO:0048869'
	
'GO:0050657'
	
'GO:0050658'
	
'GO:0050789'
	
'GO:0050794'
	
'GO:0050896'
	
'GO:0051028'
	
'GO:0051128'
	
'GO:0051129'
	
'GO:0051169'
	
'GO:0051170'
	
'GO:0051171'
	
'GO:0051172'
	
'GO:0051173'
	
'GO:0051179'
	
'GO:0051186'
	
'GO:0051234'
	
'GO:0051236'
	
'GO:0051246'
	
'GO:0051252'
	
'GO:0051253'
	
'GO:0051254'
	
'GO:0051276'
	
'GO:0051301'
	
'GO:0051321'
	
'GO:0051641'
	
'GO:0051649'
	
'GO:0051716'
	
'GO:0051726'
	
'GO:0051783'
	
'GO:0055086'
	
'GO:0055114'
	
'GO:0060249'
	
'GO:0060255'
	
'GO:0061024'
	
'GO:0065003'
	
'GO:0065004'
	
'GO:0065007'
	
'GO:0065008'
	
'GO:0065009'
	
'GO:0070271'
	
'GO:0070727'
	
'GO:0070887'
	
'GO:0071702'
	
'GO:0071704'
	
'GO:0071705'
	
'GO:0071822'
	
'GO:0071824'
	
'GO:0071840'
	
'GO:0072594'
	
'GO:0080090'
	
'GO:0090304'
	
'GO:0090305'
	
'GO:0090407'
	
'GO:0097659'
	
'GO:0098813'
	
'GO:1901135'
	
'GO:1901360'
	
'GO:1901361'
	
'GO:1901362'
	
'GO:1901564'
	
'GO:1901566'
	
'GO:1901575'
	
'GO:1901576'
	
'GO:1901605'
	
'GO:1901657'
	
'GO:1901987'
	
'GO:1902578'
	
'GO:1902580'
	
'GO:1902582'
	
'GO:1902589'
	
'GO:1902593'
	
'GO:1902679'
	
'GO:1902680'
	
'GO:1903046'
	
'GO:1903047'
	
'GO:1903506'
	
'GO:1903507'
	
'GO:1903508'
	
'GO:2000112'
	
'GO:2000113'
	
'GO:2001141'

In [16]:

    

goID <- "GO:0006914"
gene.universe <- genes(GOdata)
go.genes <- genesInTerm(GOdata, goID)[[1]]
sig.genes <- sigGenes(GOdata)

my.group <- new("classicCount", testStatistic = GOFisherTest, name = "fisher",
                 allMembers = gene.universe, groupMembers = go.genes,
                 sigMembers = sig.genes)
t <- contTable(my.group)

library(gridExtra)
grid.table(t)

runTest(my.group)


    

    





0.000111024375808973






    

In [13]:

    

enrichedGOTerms <- function(genes, allGenes, cutoff, correction, ont, mapping, ID, algorithm){
    interestingGenes <- factor(as.integer(allGenes %in% genes))
    names(interestingGenes) <- allGenes
    
    GOdata <- new("topGOdata", description=sprintf("topGO object"),
              ontology = ont, allGenes = interestingGenes,
              annotationFun = annFUN.org, mapping = mapping, 
              ID = ID, nodeSize = 10)
    
    result <- runTest(GOdata, algorithm = algorithm, statistic = "fisher")
    if (correction){
        GOs <- score(result)[which(p.adjust(score(result), method="BH") <= cutoff)]
    } else {
        GOs <- score(result)[score(result) <= cutoff]
    }
    
    plot <- showSigOfNodes(GOdata, score(result), firstSigNodes = 10, useInfo ='all', swPlot = FALSE)
    
    return(list(GOdata, GOs, plot))
}


    

In [14]:

    

enrichedGOs  <- sapply(g, enrichedGOTerms, allGenes=allGenes, 
                      cutoff=0.01, correction=FALSE, ont=ont, mapping=mapping, ID=ID, algorithm="elim")


    

    




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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

			 -- Elim Algorithm -- 

		 the algorithm is scoring 252 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

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

	 Level 10:	5 nodes to be scored	(0 eliminated genes)

	 Level 9:	10 nodes to be scored	(0 eliminated genes)

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

	 Level 7:	33 nodes to be scored	(20 eliminated genes)

	 Level 6:	46 nodes to be scored	(21 eliminated genes)

	 Level 5:	53 nodes to be scored	(28 eliminated genes)

	 Level 4:	44 nodes to be scored	(46 eliminated genes)

	 Level 3:	26 nodes to be scored	(46 eliminated genes)

	 Level 2:	11 nodes to be scored	(50 eliminated genes)

	 Level 1:	1 nodes to be scored	(50 eliminated genes)
Loading required package: Rgraphviz
Loading required package: grid

Attaching package: ‘grid’

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

    depth


Attaching package: ‘Rgraphviz’

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

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to


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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

			 -- Elim Algorithm -- 

		 the algorithm is scoring 275 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

	 Level 11:	6 nodes to be scored	(0 eliminated genes)

	 Level 10:	6 nodes to be scored	(0 eliminated genes)

	 Level 9:	12 nodes to be scored	(0 eliminated genes)

	 Level 8:	19 nodes to be scored	(0 eliminated genes)

	 Level 7:	34 nodes to be scored	(0 eliminated genes)

	 Level 6:	51 nodes to be scored	(0 eliminated genes)

	 Level 5:	57 nodes to be scored	(26 eliminated genes)

	 Level 4:	47 nodes to be scored	(26 eliminated genes)

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

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

	 Level 1:	1 nodes to be scored	(26 eliminated genes)

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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

			 -- Elim Algorithm -- 

		 the algorithm is scoring 225 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

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

	 Level 10:	4 nodes to be scored	(0 eliminated genes)

	 Level 9:	8 nodes to be scored	(0 eliminated genes)

	 Level 8:	14 nodes to be scored	(0 eliminated genes)

	 Level 7:	25 nodes to be scored	(0 eliminated genes)

	 Level 6:	37 nodes to be scored	(0 eliminated genes)

	 Level 5:	53 nodes to be scored	(36 eliminated genes)

	 Level 4:	44 nodes to be scored	(45 eliminated genes)

	 Level 3:	23 nodes to be scored	(45 eliminated genes)

	 Level 2:	9 nodes to be scored	(45 eliminated genes)

	 Level 1:	1 nodes to be scored	(45 eliminated genes)

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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

			 -- Elim Algorithm -- 

		 the algorithm is scoring 250 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

	 Level 10:	6 nodes to be scored	(11 eliminated genes)

	 Level 9:	12 nodes to be scored	(22 eliminated genes)

	 Level 8:	17 nodes to be scored	(22 eliminated genes)

	 Level 7:	29 nodes to be scored	(31 eliminated genes)

	 Level 6:	45 nodes to be scored	(73 eliminated genes)

	 Level 5:	58 nodes to be scored	(73 eliminated genes)

	 Level 4:	42 nodes to be scored	(92 eliminated genes)

	 Level 3:	22 nodes to be scored	(92 eliminated genes)

	 Level 2:	8 nodes to be scored	(92 eliminated genes)

	 Level 1:	1 nodes to be scored	(92 eliminated genes)

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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

			 -- Elim Algorithm -- 

		 the algorithm is scoring 276 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

	 Level 11:	6 nodes to be scored	(0 eliminated genes)

	 Level 10:	5 nodes to be scored	(12 eliminated genes)

	 Level 9:	11 nodes to be scored	(12 eliminated genes)

	 Level 8:	19 nodes to be scored	(12 eliminated genes)

	 Level 7:	33 nodes to be scored	(24 eliminated genes)

	 Level 6:	51 nodes to be scored	(28 eliminated genes)

	 Level 5:	60 nodes to be scored	(28 eliminated genes)

	 Level 4:	48 nodes to be scored	(28 eliminated genes)

	 Level 3:	26 nodes to be scored	(38 eliminated genes)

	 Level 2:	11 nodes to be scored	(38 eliminated genes)

	 Level 1:	1 nodes to be scored	(38 eliminated genes)

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

Build GO DAG topology ..........
	( 1846 GO terms and 4079 relations. )

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

			 -- Elim Algorithm -- 

		 the algorithm is scoring 271 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

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

	 Level 10:	5 nodes to be scored	(0 eliminated genes)

	 Level 9:	11 nodes to be scored	(0 eliminated genes)

	 Level 8:	16 nodes to be scored	(0 eliminated genes)

	 Level 7:	34 nodes to be scored	(0 eliminated genes)

	 Level 6:	51 nodes to be scored	(0 eliminated genes)

	 Level 5:	60 nodes to be scored	(0 eliminated genes)

	 Level 4:	49 nodes to be scored	(10 eliminated genes)

	 Level 3:	25 nodes to be scored	(10 eliminated genes)

	 Level 2:	11 nodes to be scored	(10 eliminated genes)

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

In [23]:

    

lengths(enrichedGOs)


    

    






	
29
	
50
	
68
	
28
	
32
	
21
	
41
	
60
	
47
	
34
	
26

In [15]:

    

enrichedGOs[[2,1]]


    

    






	
GO:0006914
		
0.000111024375808973
	
GO:0006605
		
4.74925119630649e-05
	
GO:0016192
		
0.00087861623591962
	
GO:0007033
		
0.00200880989377714
	
GO:0007034
		
0.000101229244111927
	
GO:0015031
		
0.00717492505664814
	
GO:0072594
		
8.75731737522821e-05

In [17]:

    

lengths(g)


    

    






	
34
	
58
	
146
	
88
	
146
	
72
	
188
	
102
	
194
	
27
	
65
	
75
	
103
	
51
	
50
	
67
	
43
	
37
	
52
	
49

In [72]:

    

head(shortest.path)


    

    






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In [ ]:

    

mgeneSim(g[[1]], semData=scGO, measure="Wang")


    

In [78]:

    

mgoSim(names(enrichedGOs[[1]]), names(enrichedGOs[[2]]), semData=scGO, measure="Resnik", combine="BMA")


    

    





0.031

In [79]:

    

mgoSim(names(enrichedGOs[[1]]), names(enrichedGOs[[32]]), semData=scGO, measure="Resnik", combine="BMA")


    

    





0.075

In [55]:

    

clusterSim(g[[1]], g[[2]], semData=scGO, measure="Wang", combine=NULL)


    

    






GO:0032049
GO:0006809
GO:0016226
GO:0045429
GO:0055114
GO:1901300
GO:0001402
GO:0006970
GO:0006972
GO:0007232
⋯
GO:0015918
GO:0035376
GO:0035690
GO:0033617
GO:0016050
GO:0016485
GO:0030433
GO:0031503
GO:0007097
GO:0031578

	
GO:0000077
0.121
0.094
0.121
0.050
0.161
0.191
0.311
0.282
0.242
0.371
⋯    
0.094
0.087
0.289
0.072
0.144
0.049
0.280
0.067
0.049
0.112
	
GO:0001302
0.170
0.121
0.160
0.062
0.230
0.114
0.274
0.100
0.087
0.220
⋯    
0.131
0.124
0.171
0.094
0.198
0.066
0.175
0.093
0.065
0.069
	
GO:0006457
0.129
0.198
0.276
0.093
0.191
0.079
0.211
0.186
0.163
0.172
⋯    
0.100
0.098
0.305
0.156
0.374
0.119
0.120
0.181
0.117
0.045
	
GO:0033194
0.036
0.060
0.084
0.028
0.110
0.211
0.129
0.411
0.355
0.177
⋯    
0.061
0.058
0.309
0.048
0.094
0.070
0.174
0.100
0.069
0.014
	
GO:0034599
0.073
0.111
0.143
0.059
0.089
0.326
0.250
0.334
0.290
0.351
⋯    
0.053
0.050
0.582
0.087
0.173
0.059
0.296
0.081
0.058
0.030
	
GO:0042262
0.249
0.229
0.141
0.143
0.254
0.178
0.278
0.176
0.155
0.326
⋯    
0.079
0.074
0.192
0.058
0.094
0.197
0.422
0.046
0.037
0.126
	
GO:0045454
0.160
0.114
0.147
0.176
0.198
0.206
0.478
0.089
0.078
0.395
⋯    
0.119
0.112
0.156
0.090
0.176
0.061
0.166
0.082
0.060
0.125
	
GO:0061077
0.106
0.166
0.229
0.079
0.156
0.067
0.176
0.153
0.133
0.142
⋯    
0.083
0.080
0.251
0.128
0.304
0.097
0.101
0.146
0.095
0.038
	
GO:0006378
0.151
0.243
0.143
0.137
0.117
0.035
0.073
0.052
0.044
0.059
⋯    
0.032
0.029
0.091
0.054
0.100
0.259
0.197
0.046
0.034
0.082
	
GO:0016973
0.081
0.062
0.081
0.035
0.147
0.033
0.068
0.044
0.038
0.053
⋯    
0.348
0.317
0.036
0.025
0.039
0.175
0.105
0.134
0.201
0.046
	
GO:0043488
0.085
0.100
0.141
0.137
0.175
0.067
0.166
0.089
0.077
0.135
⋯    
0.053
0.050
0.069
0.043
0.078
0.279
0.106
0.082
0.059
0.085
	
GO:0045945
0.138
0.223
0.113
0.432
0.060
0.091
0.111
0.027
0.023
0.092
⋯    
0.018
0.016
0.047
0.030
0.050
0.133
0.112
0.023
0.019
0.102
	
GO:1900152
0.085
0.138
0.076
0.195
0.059
0.061
0.116
0.026
0.022
0.096
⋯    
0.017
0.015
0.048
0.030
0.050
0.109
0.196
0.023
0.018
0.226
	
GO:1900364
0.095
0.155
0.088
0.198
0.069
0.060
0.122
0.030
0.026
0.099
⋯    
0.019
0.017
0.055
0.033
0.058
0.159
0.127
0.026
0.020
0.145
	
GO:0009228
0.265
0.322
0.158
0.198
0.180
0.070
0.127
0.038
0.033
0.105
⋯    
0.058
0.053
0.071
0.046
0.075
0.085
0.170
0.034
0.027
0.071
	
GO:0000725
0.258
0.245
0.155
0.144
0.277
0.167
0.249
0.182
0.157
0.288
⋯    
0.081
0.075
0.201
0.063
0.108
0.208
0.412
0.049
0.039
0.121
	
GO:0000730
0.171
0.196
0.309
0.109
0.220
0.115
0.188
0.156
0.129
0.206
⋯    
0.061
0.055
0.167
0.309
0.210
0.157
0.281
0.043
0.033
0.096
	
GO:0043007
0.257
0.249
0.245
0.144
0.291
0.086
0.170
0.057
0.050
0.140
⋯    
0.084
0.079
0.098
0.163
0.303
0.217
0.308
0.052
0.040
0.190
	
GO:0007533
0.201
0.137
0.172
0.079
0.342
0.089
0.180
0.067
0.059
0.148
⋯    
0.100
0.095
0.104
0.064
0.114
0.110
0.207
0.062
0.048
0.072
	
GO:0008298
0.036
0.060
0.084
0.028
0.110
0.024
0.060
0.108
0.093
0.048
⋯    
0.215
0.205
0.081
0.048
0.094
0.070
0.036
0.383
0.252
0.014
	
GO:0055085
0.186
0.126
0.162
0.067
0.224
0.127
0.285
0.098
0.086
0.235
⋯    
0.530
0.501
0.173
0.100
0.196
0.068
0.188
0.193
0.222
0.078
	
GO:0000147
0.133
0.090
0.378
0.052
0.149
0.098
0.202
0.065
0.057
0.166
⋯    
0.095
0.088
0.118
0.302
0.377
0.046
0.142
0.060
0.046
0.124
	
GO:0006897
0.034
0.058
0.086
0.026
0.115
0.022
0.059
0.113
0.096
0.046
⋯    
0.316
0.299
0.082
0.046
0.097
0.070
0.033
0.235
0.262
0.012
	
GO:0030041
0.083
0.068
0.277
0.037
0.113
0.065
0.141
0.052
0.044
0.109
⋯    
0.066
0.059
0.090
0.540
0.298
0.034
0.097
0.046
0.034
0.082
	
GO:0000288
0.125
0.216
0.126
0.119
0.105
0.029
0.062
0.046
0.038
0.049
⋯    
0.027
0.024
0.080
0.044
0.087
0.183
0.285
0.040
0.029
0.109
	
GO:0034629
0.030
0.051
0.071
0.024
0.091
0.021
0.051
0.089
0.076
0.040
⋯    
0.176
0.166
0.067
0.041
0.077
0.058
0.030
0.672
0.206
0.012
	
GO:0051654
0.034
0.054
0.076
0.027
0.095
0.023
0.055
0.094
0.081
0.044
⋯    
0.196
0.186
0.072
0.045
0.082
0.063
0.034
0.195
0.645
0.013
	
GO:0006890
0.052
0.042
0.059
0.020
0.164
0.038
0.095
0.072
0.061
0.071
⋯    
0.413
0.381
0.055
0.034
0.062
0.047
0.057
0.146
0.305
0.022
	
GO:0000086
0.115
0.088
0.115
0.045
0.165
0.083
0.195
0.072
0.061
0.152
⋯    
0.093
0.085
0.123
0.065
0.139
0.046
0.127
0.065
0.046
0.186
	
GO:0006355
0.170
0.267
0.136
0.354
0.074
0.075
0.142
0.033
0.028
0.119
⋯    
0.022
0.020
0.058
0.037
0.061
0.164
0.136
0.029
0.023
0.135
	
GO:0019918
0.132
0.156
0.153
0.080
0.136
0.031
0.073
0.060
0.050
0.056
⋯    
0.033
0.030
0.097
0.050
0.109
0.273
0.212
0.052
0.037
0.074
	
GO:0034969
0.198
0.131
0.189
0.080
0.220
0.070
0.132
0.043
0.037
0.107
⋯    
0.064
0.059
0.075
0.149
0.231
0.210
0.288
0.039
0.030
0.167
	
GO:0044257
0.186
0.184
0.167
0.104
0.138
0.041
0.085
0.061
0.052
0.070
⋯    
0.038
0.035
0.108
0.064
0.119
0.343
0.610
0.055
0.041
0.259
	
GO:0051726
0.164
0.125
0.164
0.186
0.221
0.211
0.516
0.102
0.089
0.421
⋯    
0.127
0.119
0.176
0.098
0.202
0.068
0.170
0.095
0.067
0.179
	
GO:0034605
0.074
0.113
0.147
0.059
0.092
0.176
0.255
0.472
0.408
0.414
⋯    
0.054
0.051
0.352
0.088
0.178
0.061
0.253
0.083
0.060
0.030
	
GO:0008150
0.091
0.142
0.213
0.061
0.329
0.052
0.148
0.318
0.282
0.120
⋯    
0.161
0.162
0.223
0.116
0.289
0.199
0.080
0.323
0.193
0.030
	
GO:0006446
0.184
0.302
0.155
0.375
0.086
0.080
0.153
0.038
0.033
0.129
⋯    
0.026
0.024
0.071
0.047
0.075
0.201
0.181
0.034
0.028
0.175
	
GO:0019509
0.266
0.242
0.165
0.144
0.187
0.055
0.111
0.039
0.033
0.087
⋯    
0.051
0.045
0.070
0.042
0.075
0.129
0.174
0.034
0.026
0.066
	
GO:0016579
0.168
0.174
0.170
0.091
0.153
0.035
0.081
0.067
0.057
0.064
⋯    
0.039
0.036
0.106
0.057
0.120
0.466
0.323
0.060
0.043
0.124
	
GO:1902499
0.099
0.111
0.101
0.247
0.082
0.101
0.142
0.036
0.030
0.113
⋯    
0.022
0.019
0.064
0.036
0.069
0.182
0.167
0.031
0.023
0.131
	
GO:0000055
0.046
0.033
0.114
0.019
0.113
0.035
0.075
0.050
0.043
0.058
⋯    
0.285
0.260
0.040
0.090
0.088
0.035
0.050
0.101
0.344
0.031
	
GO:0006606
0.042
0.029
0.036
0.018
0.091
0.035
0.065
0.040
0.035
0.052
⋯    
0.332
0.306
0.033
0.025
0.035
0.030
0.047
0.185
0.193
0.023
	
GO:0006999
0.068
0.107
0.301
0.054
0.092
0.047
0.113
0.090
0.077
0.091
⋯    
0.051
0.048
0.153
0.384
0.550
0.059
0.069
0.083
0.057
0.077
	
GO:0051292
0.048
0.075
0.306
0.041
0.057
0.036
0.078
0.057
0.048
0.063
⋯    
0.034
0.031
0.099
0.620
0.342
0.038
0.051
0.051
0.037
0.061

In [52]:

    

clusterSim <- mclusterSim(g, semData=scGO, measure="Wang", combine="BMA")


    

In [53]:

    

head(clusterSim)


    

    







	
1.000
0.603
0.638
0.574
0.654
0.627
	
0.603
1.000
0.715
0.641
0.701
0.748
	
0.638
0.715
1.000
0.660
0.726
0.718
	
0.574
0.641
0.660
1.000
0.642
0.626
	
0.654
0.701
0.726
0.642
1.000
0.676
	
0.627
0.748
0.718
0.626
0.676
1.000

In [54]:

    

head(shortest.path)


    

    






V1
V2
V3
V4
V5
V6

	
0
1
1
1
1
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1
0
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1
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1
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1
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0
2
	
1
2
1
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2
0

In [5]:

    

pathways <- read.table("../biochemical_pathways.tab", sep="\t")
cols <- c("pathway_name", "enzyme_name", "E.C._reaction_number", "gene_name", "reference")
colnames(pathways) <- cols

toGene <- function(ORFIdentifiers){
    genes <- character()
    for (identifier in ORFIdentifiers){
        gene <- character()
        try(
            gene <- as.character(org.Sc.sgdGENENAME[identifier])
        )
        genes <- c(genes, gene)
    }
    return(genes)
}

toPath <- function(ORFIdentifiers){
    paths <- character()
    for (identifier in ORFIdentifiers){
        path <- character()
        try(
            path <- as.character(org.Sc.sgdPATH[identifier])
        )
        paths <- c(paths, path)
    }
    return(paths)
}

get_pathways <- function(ORFIdentifiers, pathways) {
    genes  <- toGene(ORFIdentifiers)
    return(subset(pathways, gene_name %in% genes)$pathway_name)
}

get_pathway_genes <- function(ORFIdentifiers, pathways) {
    genes  <- toGene(ORFIdentifiers)
    return(subset(pathways, gene_name %in% genes)$gene_name)
}


    

In [ ]:

    

pathway_list <- sapply(g, get_pathways, pathways)
pathway_genes <- sapply(g, get_pathway_genes, pathways)


    

In [140]:

    

enrichedGOsPathway <- sapply(pathway_genes[lengths(pathway_genes) > 0], enrichedGOTerms, allGenes=allGeneNames, 
                      cutOff=cutOff, correction=correction, ont=ont, mapping=mapping, ID=ID)


    

    




Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 92 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 67 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 264 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 209 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 126 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 61 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 221 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 96 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 168 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 44 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 30 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 95 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

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

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 129 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 82 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 191 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 105 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 41 nontrivial nodes
		 parameters: 
			 test statistic: fisher

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

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

Building most specific GOs .....
	( 1679 GO terms found. )

Build GO DAG topology ..........
	( 3637 GO terms and 8228 relations. )

Annotating nodes ...............
	( 1439 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 77 nontrivial nodes
		 parameters: 
			 test statistic: fisher

In [141]:

    

range <- 1:length(enrichedGOsPathway)

simsPathway <- sapply(range, function(i) sapply(range, function(j) 
                    mgoSim(names(enrichedGOsPathway[[i]]),
                        names(enrichedGOsPathway[[j]]),
                        semData=scGO, measure="Wang", combine="BMA")))


    

In [142]:

    

head(simsPathway)


    

    







	
1.000
0.763
0.843
0.824
0.859
0.763
0.836
0.772
0.843
0.524
0.579
0.743
0.801
0.727
0.790
0.791
0.788
0.628
0.871
0.665
	
0.763
1.000
0.769
0.707
0.719
0.742
0.718
0.745
0.822
0.584
0.727
0.804
0.856
0.649
0.631
0.653
0.707
0.466
0.723
0.565
	
0.843
0.769
1.000
0.961
0.765
0.801
0.930
0.788
0.844
0.534
0.570
0.713
0.862
0.669
0.827
0.829
0.898
0.450
0.886
0.678
	
0.824
0.707
0.961
1.000
0.741
0.763
0.926
0.760
0.823
0.509
0.533
0.664
0.828
0.659
0.857
0.828
0.902
0.448
0.872
0.675
	
0.859
0.719
0.765
0.741
1.000
0.595
0.740
0.618
0.772
0.453
0.481
0.657
0.775
0.700
0.710
0.755
0.686
0.590
0.724
0.558
	
0.763
0.742
0.801
0.763
0.595
1.000
0.783
0.746
0.773
0.550
0.662
0.667
0.722
0.558
0.671
0.619
0.776
0.406
0.785
0.697

In [118]:

    

head(shortest.path)


    

    






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In [151]:

    

enrichedGOs[[1]]


    

    






	
GO:0006508
		
0.0305666626725701
	
GO:0009057
		
0.0268263523123756
	
GO:0009896
		
0.0275243318688756
	
GO:0019538
		
0.037645201260442
	
GO:0030163
		
0.038000496959972
	
GO:0035966
		
0.0369152752689263
	
GO:0035967
		
0.0232568990511012
	
GO:0042176
		
0.0192941639335425
	
GO:0043632
		
0.0317229083283707
	
GO:0070646
		
0.00379354097137652
	
GO:0070647
		
0.0151356737247353

In [ ]:

    

geneSimilarities <- sapply(allGenes, function(i) sapply(allGenes, function(j) geneSim(i, j, semData=scGO, combine="BMA")))


    

In [ ]:

    

geneSimilarities


    

In [6]:

    

cutOff <- 0.05

filename <- sprintf("%s-%s-%s-%s.rda", file, p, cutOff, ont)

if (file.exists(filename)){
    
    print(sprintf("loading: %s", filename))
    load(filename)
    print("loaded")
    
} else {
    
    print("creating topGO objects")

    geneLists <- vector("list", numCom) 
    GOdataObjects <- vector("list", numCom) 
    resultFishers <- vector("list", numCom) 
    results <- vector("list", numCom) 
    gos <- vector("list", numCom) 

    #perform enrichment analyses
    for (c in 1:numCom){

        #factor of interesting genes
        geneList <- factor(as.integer(allGenes %in% g[[c]]))
        names(geneList) <- allGenes
        geneLists[[c]] <- geneList

        #construct topGO object
        GOdata <- new("topGOdata", description=sprintf("topGO object for community %s", c),
                      ontology = ont, allGenes = geneList,
                      annotationFun = annFUN.org, mapping = mapping, 
                      ID = ID, nodeSize = 10)
        GOdataObjects[[c]] <- GOdata

        #fishers exact test classic
        resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
        resultFishers[[c]] <- resultFisher

        #tabulate results
        allRes <- GenTable(GOdata, classicFisher = resultFisher,
                      orderBy = "classicFisher")
        results[[c]] <- allRes
        
        #go terms < cut off  Benjamini-Hochberg multiple hypothesis corrected pval
        gos[[c]] <- score(resultFisher)[which(p.adjust(score(resultFisher), method="BH") <= cutOff)]

        print(sprintf("community %s complete", c))
    }
    
    print(sprintf("Saving data: %s", filename))
    save(geneLists, GOdataObjects, resultFishers, results, gos, file=filename)
    print("saved")
}


    

    




[1] "creating topGO objects"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 355 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 1 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 581 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 2 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 835 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 3 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 681 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 4 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 586 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 5 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 644 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 6 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 877 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 7 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 706 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 8 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 831 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 9 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 408 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 10 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 516 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 11 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 567 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 12 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 706 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 13 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 531 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 14 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 473 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 15 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 612 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 16 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 577 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 17 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 501 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 18 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 463 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 19 complete"






    




Building most specific GOs .....
	( 1689 GO terms found. )

Build GO DAG topology ..........
	( 3643 GO terms and 8240 relations. )

Annotating nodes ...............
	( 1558 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 602 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    




[1] "community 20 complete"
[1] "Saving data: yeast_union-0.7-0.05-BP.rda"
[1] "saved"

In [7]:

    

print_accession_number <- function(terms, file){
    for (s in strsplit(names(terms), ":")){
        write(s[2], file=file, append=TRUE)
    }
}


    

In [8]:

    

###write accession number to file
for (i in 1:length(gos)){
    accessionFile <- sprintf("accession_numbers-%s-%s-%s", cutOff, ont, i)
    print_accession_number(gos[[i]], file=accessionFile)
}


    

In [10]:

    

wangAllGeneSim <- mgeneSim(allGenes, semData=scGO, measure="Wang", combine="BMA", verbose=TRUE)


    

    




  |======================================================================| 100%

In [11]:

    

clusters <- hclust(as.dist(-log(wangAllGeneSim)))
clusterCut <- cutree(clusters, numCom)


    

In [12]:

    

plot(clusters)


    

In [13]:

    

assignedCommunities <- numeric(length(allGenes))
names(assignedCommunities) <- allGenes

for (i in 1:numCom){
    for (geneName in g[[i]]){
        assignedCommunities[geneName] <- i
    }
}


    

In [14]:

    

library(NMI)


    

In [15]:

    

assignedCommunities <- assignedCommunities[names(assignedCommunities) %in% names(clusterCut)]


    

In [16]:

    

assignedCommunitiesDF <- data.frame(assignedCommunities)
assignedCommunitiesDF <- cbind(Row.Names = rownames(assignedCommunitiesDF), assignedCommunitiesDF)


    

In [17]:

    

clusterCutDF <- data.frame(clusterCut)
clusterCutDF <- cbind(Row.Names = rownames(clusterCutDF), clusterCutDF)


    

In [18]:

    

NMI(assignedCommunitiesDF, clusterCutDF)


    

    





$value = 0.0711074542082947

In [98]:

    

most_representative_term_weighted <- function(namedTerms){
    
    counts <- numeric(length(namedTerms))
    names(counts) <- names(namedTerms)

    for (term in names(namedTerms)) {
        ancestors <- as.list(GOBPANCESTOR[term])
        for (ancestor in ancestors[[term]]) {
            if (ancestor %in% names(counts)) {
                counts[ancestor] <- counts[ancestor] + 1
            }
        }

    }
#     return (sort(counts / sum(counts), decreasing=TRUE))
    return (sort(counts / max(counts), decreasing=TRUE))
}


    

In [33]:

    

most_representative_term_ancestor <- function(namedTerms){
    
    counts <- numeric(length(namedTerms))
    names(counts) <- names(namedTerms)

    for (term in names(namedTerms)) {
        ancestors <- as.list(GOBPANCESTOR[term])
        for (ancestor in ancestors[[term]]) {
            if (ancestor %in% names(counts)) {
                counts[ancestor] <- counts[ancestor] + 1
            }
        }

    }
#     return (sort(counts / sum(counts), decreasing=TRUE))
    return (names(sort(counts / sum(counts), decreasing=TRUE)[1]))
}


    

In [34]:

    

representativeTermsAncestor <- sapply(Filter(length, gos), most_representative_term_ancestor)


    

In [35]:

    

select(GO.db, keys=representativeTermsAncestor, columns=c("TERM", "DEFINITION"))


    

    




'select()' returned many:1 mapping between keys and columns






    






GOID
TERM
DEFINITION

	
GO:0006644                                                                                                                                                                                                                                                                                                                                                                                                          
phospholipid metabolic process                                                                                                                                                                                                                                                                                                                                                                                      
The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.                                                                                                                                                                                                                                                                                            
	
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.        
	
GO:0044699                                                                                                                                                                                                                                                                                                                                                                                                          
single-organism process                                                                                                                                                                                                                                                                                                                                                                                             
A biological process that involves only one organism.                                                                                                                                                                                                                                                                                                                                                               
	
GO:0044710                                                                                                                                                                                                                                                                                                                                                                                                          
single-organism metabolic process                                                                                                                                                                                                                                                                                                                                                                                   
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.                                                                                                                                                                                                                              
	
GO:0051128                                                                                                                                                                                                                                                                                                                                                                                                          
regulation of cellular component organization                                                                                                                                                                                                                                                                                                                                                                       
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.                                                                                                                              
	
GO:0034641                                                                                                                                                                                                                                                                                                                                                                                                          
cellular nitrogen compound metabolic process                                                                                                                                                                                                                                                                                                                                                                        
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.                                                                                                                                                                                                                                                                              
	
GO:0006725                                                                                                                                                                                                                                                                                                                                                                                                          
cellular aromatic compound metabolic process                                                                                                                                                                                                                                                                                                                                                                        
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.                                                                                                                                                                  
	
GO:0044710                                                                                                                                                                                                                                                                                                                                                                                                          
single-organism metabolic process                                                                                                                                                                                                                                                                                                                                                                                   
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.                                                                                                                                                                                                                              
	
GO:0044238                                                                                                                                                                                                                                                                                                                                                                                                          
primary metabolic process                                                                                                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.                                                                                                                                                                                                     
	
GO:0044699                                                                                                                                                                                                                                                                                                                                                                                                          
single-organism process                                                                                                                                                                                                                                                                                                                                                                                             
A biological process that involves only one organism.                                                                                                                                                                                                                                                                                                                                                               
	
GO:0005975                                                                                                                                                                                                                                                                                                                                                                                                          
carbohydrate metabolic process                                                                                                                                                                                                                                                                                                                                                                                      
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.                                                                                                                                                           
	
GO:0044710                                                                                                                                                                                                                                                                                                                                                                                                          
single-organism metabolic process                                                                                                                                                                                                                                                                                                                                                                                   
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.                                                                                                                                                                                                                              
	
GO:0030029                                                                                                                                                                                                                                                                                                                                                                                                          
actin filament-based process                                                                                                                                                                                                                                                                                                                                                                                        
Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.                                                                                                                                                                                                                                                    
	
GO:0051726                                                                                                                                                                                                                                                                                                                                                                                                          
regulation of cell cycle                                                                                                                                                                                                                                                                                                                                                                                            
Any process that modulates the rate or extent of progression through the cell cycle.                                                                                                                                                                                                                                                                                                                                
	
GO:0016070                                                                                                                                                                                                                                                                                                                                                                                                          
RNA metabolic process                                                                                                                                                                                                                                                                                                                                                                                               
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.                                                                                                                                                                          
	
GO:0044085                                                                                                                                                                                                                                                                                                                                                                                                          
cellular component biogenesis                                                                                                                                                                                                                                                                                                                                                                                       
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.                                                                                                 
	
GO:0044763                                                                                                                                                                                                                                                                                                                                                                                                          
single-organism cellular process                                                                                                                                                                                                                                                                                                                                                                                    
Any process that is carried out at the cellular level, occurring within a single organism.                                                                                                                                                                                                                                                                                                                          
	
GO:0048518                                                                                                                                                                                                                                                                                                                                                                                                          
positive regulation of biological process                                                                                                                                                                                                                                                                                                                                                                           
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.                                                                                                                                         
	
GO:0016070                                                                                                                                                                                                                                                                                                                                                                                                          
RNA metabolic process                                                                                                                                                                                                                                                                                                                                                                                               
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.                                                                                                                                                                          
	
GO:0051716                                                                                                                                                                                                                                                                                                                                                                                                          
cellular response to stimulus                                                                                                                                                                                                                                                                                                                                                                                       
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 stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.                                                                                                                     
	
GO:0009893                                                                                                                                                                                                                                                                                                                                                                                                          
positive regulation of metabolic process                                                                                                                                                                                                                                                                                                                                                                            
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.                                                                                                                                                                                                                                                                          
	
GO:0009056                                                                                                                                                                                                                                                                                                                                                                                                          
catabolic process                                                                                                                                                                                                                                                                                                                                                                                                   
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.                                                                                                                                                                                                                            
	
GO:0042221                                                                                                                                                                                                                                                                                                                                                                                                          
response to chemical                                                                                                                                                                                                                                                                                                                                                                                                
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 chemical stimulus.                                                                                                                                                                                                                  
	
GO:0051179                                                                                                                                                                                                                                                                                                                                                                                                          
localization                                                                                                                                                                                                                                                                                                                                                                                                        
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.                                                                                                                                         
	
GO:0061024                                                                                                                                                                                                                                                                                                                                                                                                          
membrane organization                                                                                                                                                                                                                                                                                                                                                                                               
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.                                                                                                                  
	
GO:0050789                                                                                                                                                                                                                                                                                                                                                                                                          
regulation of biological process                                                                                                                                                                                                                                                                                                                                                                                    
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.                                                                                                                                                      
	
GO:0006629                                                                                                                                                                                                                                                                                                                                                                                                          
lipid metabolic process                                                                                                                                                                                                                                                                                                                                                                                             
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	
GO:0065007                                                                                                                                                                                                                                                                                                                                                                                                          
biological regulation                                                                                                                                                                                                                                                                                                                                                                                               
Any process that modulates a measurable attribute of any biological process, quality or function.                                                                                                                                                                                                                                                                                                                   
	
GO:0018130                                                                                                                                                                                                                                                                                                                                                                                                          
heterocycle biosynthetic process                                                                                                                                                                                                                                                                                                                                                                                    
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).                                                                                                                                                                                                                          
	
GO:0008152                                                                                                                                                                                                                                                                                                                                                                                                          
metabolic process                                                                                                                                                                                                                                                                                                                                                                                                   
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.                                                                                                     
	
GO:0007031                                                                                                                                                                                                                                                                                                                                                                                                          
peroxisome organization                                                                                                                                                                                                                                                                                                                                                                                             
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.                                                                                                                                                      
	
GO:0065007                                                                                                                                                                                                                                                                                                                                                                                                          
biological regulation                                                                                                                                                                                                                                                                                                                                                                                               
Any process that modulates a measurable attribute of any biological process, quality or function.                                                                                                                                                                                                                                                                                                                   
	
GO:0051179                                                                                                                                                                                                                                                                                                                                                                                                          
localization                                                                                                                                                                                                                                                                                                                                                                                                        
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.                                                                                                                                         
	
GO:0071840                                                                                                                                                                                                                                                                                                                                                                                                          
cellular component organization or biogenesis                                                                                                                                                                                                                                                                                                                                                                       
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.                                                                                                                                                                                                                                                       
	
GO:0071840                                                                                                                                                                                                                                                                                                                                                                                                          
cellular component organization or biogenesis                                                                                                                                                                                                                                                                                                                                                                       
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.                                                                                                                                                                                                                                                       
	
GO:0008152                                                                                                                                                                                                                                                                                                                                                                                                          
metabolic process                                                                                                                                                                                                                                                                                                                                                                                                   
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.                                                                                                     
	
GO:0008152                                                                                                                                                                                                                                                                                                                                                                                                          
metabolic process                                                                                                                                                                                                                                                                                                                                                                                                   
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.                                                                                                     
	
GO:0050789                                                                                                                                                                                                                                                                                                                                                                                                          
regulation of biological process                                                                                                                                                                                                                                                                                                                                                                                    
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.                                                                                                                                                      
	
GO:0043603                                                                                                                                                                                                                                                                                                                                                                                                          
cellular amide metabolic process                                                                                                                                                                                                                                                                                                                                                                                    
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.                                                                                                                                                                                                 
	
GO:0009132                                                                                                                                                                                                                                                                                                                                                                                                          
nucleoside diphosphate metabolic process                                                                                                                                                                                                                                                                                                                                                                            
The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.                                                                                                                                                                                                                     
	
GO:0009058                                                                                                                                                                                                                                                                                                                                                                                                          
biosynthetic process                                                                                                                                                                                                                                                                                                                                                                                                
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.                                                                                                                                                                                                                 
	
GO:0051179                                                                                                                                                                                                                                                                                                                                                                                                          
localization                                                                                                                                                                                                                                                                                                                                                                                                        
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.                                                                                                                                         
	
GO:0048519                                                                                                                                                                                                                                                                                                                                                                                                          
negative regulation of biological process                                                                                                                                                                                                                                                                                                                                                                           
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.                                                                                                                                    
	
GO:1901360                                                                                                                                                                                                                                                                                                                                                                                                          
organic cyclic compound metabolic process                                                                                                                                                                                                                                                                                                                                                                           
The chemical reactions and pathways involving organic cyclic compound.                                                                                                                                                                                                                                                                                                                                              
	
GO:0022402                                                                                                                                                                                                                                                                                                                                                                                                          
cell cycle process                                                                                                                                                                                                                                                                                                                                                                                                  
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.                                                                                                                                                                                                                                                                                                   
	
GO:0007163                                                                                                                                                                                                                                                                                                                                                                                                          
establishment or maintenance of cell polarity                                                                                                                                                                                                                                                                                                                                                                       
Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.                                                                                                                                                                                                                                                                 
	
GO:0043170                                                                                                                                                                                                                                                                                                                                                                                                          
macromolecule metabolic process                                                                                                                                                                                                                                                                                                                                                                                     
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.                                                                                                                                         
	
GO:0009056                                                                                                                                                                                                                                                                                                                                                                                                          
catabolic process                                                                                                                                                                                                                                                                                                                                                                                                   
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.                                                                                                                                                                                                                            
	
GO:0043170                                                                                                                                                                                                                                                                                                                                                                                                          
macromolecule metabolic process                                                                                                                                                                                                                                                                                                                                                                                     
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.                                                                                                                                         
	
GO:0051716                                                                                                                                                                                                                                                                                                                                                                                                          
cellular response to stimulus                                                                                                                                                                                                                                                                                                                                                                                       
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 stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.                                                                                                                     
	
GO:0016043                                                                                                                                                                                                                                                                                                                                                                                                          
cellular component organization                                                                                                                                                                                                                                                                                                                                                                                     
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.                                                                                                                                                                                                                                                                                                   
	
GO:0009058                                                                                                                                                                                                                                                                                                                                                                                                          
biosynthetic process                                                                                                                                                                                                                                                                                                                                                                                                
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.                                                                                                                                                                                                                 

In [36]:

    

simsGOAncestor <- mgoSim(representativeTermsAncestor, representativeTermsAncestor, semData=scGO, measure="Wang", combine=NULL)


    

In [37]:

    

head(simsGOAncestor)


    

    






GO:0006644
GO:0007049
GO:0044699
GO:0044710
GO:0051128
GO:0034641
GO:0006725
GO:0044238
GO:0005975
GO:0030029
⋯
GO:0071840
GO:0043603
GO:0009132
GO:0009058
GO:0048519
GO:1901360
GO:0022402
GO:0007163
GO:0043170
GO:0016043

	
GO:0006644
1.000
0.354
0.239
0.405
0.130
0.334
0.354
0.323
0.362
0.354
⋯    
0.106
0.294
0.618
0.197
0.087
0.281
0.339
0.354
0.281
0.184
	
GO:0007049
0.354
1.000
0.547
0.379
0.245
0.289
0.321
0.191
0.139
0.722
⋯    
0.243
0.256
0.291
0.191
0.180
0.156
0.872
0.722
0.156
0.379
	
GO:0044699
0.239
0.547
1.000
0.643
0.178
0.212
0.243
0.340
0.236
0.547
⋯    
0.444
0.192
0.198
0.340
0.304
0.276
0.493
0.547
0.276
0.286
	
GO:0044710
0.405
0.379
0.643
1.000
0.129
0.340
0.379
0.507
0.371
0.379
⋯    
0.286
0.305
0.336
0.507
0.210
0.419
0.349
0.379
0.419
0.198
	
GO:0051128
0.130
0.245
0.178
0.129
1.000
0.225
0.245
0.142
0.107
0.245
⋯    
0.400
0.198
0.107
0.142
0.447
0.117
0.229
0.245
0.117
0.651
	
GO:0034641
0.334
0.289
0.212
0.340
0.225
1.000
0.649
0.379
0.283
0.289
⋯    
0.212
0.888
0.433
0.379
0.161
0.314
0.268
0.289
0.314
0.340

In [38]:

    

head(shortest.path)


    

    






V1
V2
V3
V4
V5
V6
V7
V8
V9
V10
⋯
V43
V44
V45
V46
V47
V48
V49
V50
V51
V52

	
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⋯
5
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2
1
2
⋯
5
3
5
2
4
3
3
3
2
2
	
1
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2
2
2
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2
2
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⋯
6
2
6
3
5
4
2
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3
	
1
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⋯
6
4
6
3
5
4
4
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3
3
	
1
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1
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1
1
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⋯
4
4
4
1
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2
4
4
2
2
	
2
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1
0
1
2
2
2
⋯
5
4
5
2
4
3
4
4
1
1

In [15]:

    

information_content <- function(term){
    return (goSim(term, term, semData=scGO, measure="Resnik"))
}

most_representative_term_ic <- function(namedTerms){
    ics <- sapply(names(namedTerms), information_content)
    names(ics) <- names(namedTerms)
    return(names(sort(ics, decreasing=TRUE)[1]))
}


    

In [16]:

    

representativeTermsIC <- sapply(Filter(length, gos), most_representative_term_ic)


    

In [17]:

    

select(GO.db, keys=representativeTermsIC, columns=c("TERM", "DEFINITION"))


    

    




'select()' returned 1:1 mapping between keys and columns






    






GOID
TERM
DEFINITION

	
GO:0090114                                                                                                                                                                                                                                                                                                       
COPII-coated vesicle budding                                                                                                                                                                                                                                                                                     
The evagination of an endoplasmic reticulum membrane, resulting in formation of a COPII-coated vesicle.                                                                                                                                                                                                          
	
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.             
	
GO:0009132                                                                                                                                                                                                                                                                                                       
nucleoside diphosphate metabolic process                                                                                                                                                                                                                                                                         
The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.                                                                                                                  
	
GO:0044038                                                                                                                                                                                                                                                                                                       
cell wall macromolecule biosynthetic process                                                                                                                                                                                                                                                                     
The chemical reactions and pathways resulting in the formation of a macromolecule destined to form part of a cell wall.                                                                                                                                                                                          
	
GO:0043467                                                                                                                                                                                                                                                                                                       
regulation of generation of precursor metabolites and energy                                                                                                                                                                                                                                                     
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances.                                      
	
GO:0008033                                                                                                                                                                                                                                                                                                       
tRNA processing                                                                                                                                                                                                                                                                                                  
The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.                                                                                                                                                                                                
	
GO:0031113                                                                                                                                                                                                                                                                                                       
regulation of microtubule polymerization                                                                                                                                                                                                                                                                         
Any process that modulates the frequency, rate or extent of microtubule polymerization.                                                                                                                                                                                                                          
	
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.                                                                        
	
GO:0006896                                                                                                                                                                                                                                                                                                       
Golgi to vacuole transport                                                                                                                                                                                                                                                                                       
The directed movement of substances from the Golgi to the vacuole.                                                                                                                                                                                                                                               
	
GO:0016973                                                                                                                                                                                                                                                                                                       
poly(A)+ mRNA export from nucleus                                                                                                                                                                                                                                                                                
The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.                                                                                                                                                                                                                                    
	
GO:0006576                                                                                                                                                                                                                                                                                                       
cellular biogenic amine metabolic process                                                                                                                                                                                                                                                                        
The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.                                                            
	
GO:0002181                                                                                                                                                                                                                                                                                                       
cytoplasmic translation                                                                                                                                                                                                                                                                                          
The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.                                                                
	
GO:0040001                                                                                                                                                                                                                                                                                                       
establishment of mitotic spindle localization                                                                                                                                                                                                                                                                    
The cell cycle process in which the directed movement of the mitotic spindle to a specific location in the cell occurs.                                                                                                                                                                                          
	
GO:0016558                                                                                                                                                                                                                                                                                                       
protein import into peroxisome matrix                                                                                                                                                                                                                                                                            
The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported. The cargo protein is then released into the peroxisome matrix.
	
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:0007096                                                                                                                                                                                                                                                                                                       
regulation of exit from mitosis                                                                                                                                                                                                                                                                                  
Any process involved in the progression from anaphase/telophase to G1 that is associated with a conversion from high to low mitotic CDK activity.                                                                                                                                                                
	
GO:1904669                                                                                                                                                                                                                                                                                                       
ATP export                                                                                                                                                                                                                                                                                                       
The directed movement of ATP out of a cell or organelle.                                                                                                                                                                                                                                                         

In [18]:

    

simsGOIC <- mgoSim(representativeTermsIC, representativeTermsIC, semData=scGO, measure="Wang", combine=NULL)


    

In [19]:

    

head(simsGOIC)


    

    






GO:0090114
GO:0031146
GO:0009132
GO:0044038
GO:0043467
GO:0008033
GO:0031113
GO:0051123
GO:0006896
GO:0016973
GO:0006576
GO:0002181
GO:0040001
GO:0016558
GO:0006999
GO:0007096
GO:1904669

	
GO:0090114
1.000
0.045
0.126
0.083
0.070
0.050
0.187
0.086
0.551
0.392
0.068
0.048
0.428
0.496
0.197
0.193
0.214
	
GO:0031146
0.045
1.000
0.186
0.241
0.161
0.226
0.037
0.154
0.024
0.092
0.196
0.296
0.040
0.032
0.072
0.035
0.020
	
GO:0009132
0.126
0.186
1.000
0.193
0.192
0.404
0.102
0.294
0.065
0.112
0.350
0.247
0.119
0.097
0.089
0.106
0.056
	
GO:0044038
0.083
0.241
0.193
1.000
0.205
0.270
0.106
0.399
0.029
0.114
0.250
0.462
0.080
0.064
0.141
0.071
0.025
	
GO:0043467
0.070
0.161
0.192
0.205
1.000
0.185
0.181
0.126
0.039
0.063
0.274
0.162
0.068
0.053
0.128
0.176
0.033
	
GO:0008033
0.050
0.226
0.404
0.270
0.185
1.000
0.042
0.383
0.026
0.130
0.328
0.328
0.046
0.037
0.083
0.040
0.021

In [20]:

    

head(shortest.path)


    

    






V1
V2
V3
V4
V5
V6
V7
V8
V9
V10
V11
V12
V13
V14
V15
V16
V17
V18
V19
V20

	
0
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1
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1
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2
1
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2
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3
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3
2
3
3
4
	
1
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1
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2
1
1
1
1
1
1
2
2
1
2
1
2
2
3
	
1
1
0
2
2
1
1
2
2
2
2
2
3
3
2
2
2
3
3
4
	
1
1
2
0
1
2
2
2
2
2
2
2
3
3
2
3
2
3
3
4
	
1
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2
1
0
2
3
2
3
3
3
3
4
4
3
4
3
4
4
5
	
1
2
1
2
2
0
2
2
3
3
3
3
4
4
3
3
3
4
4
5

In [148]:

    

wangClusterSim <- mclusterSim(g, semData=scGO, measure="Wang", combine="BMA")


    

In [149]:

    

head(wangClusterSim)


    

    







	
1.000
0.527
0.544
0.491
0.534
0.491
0.513
0.495
0.448
0.505
0.375
0.632
0.531
	
0.527
1.000
0.610
0.568
0.520
0.534
0.523
0.507
0.548
0.540
0.455
0.584
0.494
	
0.544
0.610
1.000
0.625
0.523
0.608
0.651
0.606
0.634
0.602
0.358
0.604
0.391
	
0.491
0.568
0.625
1.000
0.514
0.558
0.609
0.552
0.623
0.592
0.416
0.521
0.383
	
0.534
0.520
0.523
0.514
1.000
0.496
0.514
0.522
0.464
0.585
0.409
0.554
0.453
	
0.491
0.534
0.608
0.558
0.496
1.000
0.557
0.540
0.539
0.549
0.354
0.591
0.453

In [150]:

    

head(shortest.path)


    

    






V1
V2
V3
V4
V5
V6
V7
V8
V9
V10
V11
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V13

	
0
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2
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2
1
1
1
	
1
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1
2
1
1
2
2
3
1
2
2
2
	
1
1
0
1
1
2
2
2
3
2
2
2
2
	
1
2
1
0
2
3
1
2
2
3
2
2
2
	
2
1
1
2
0
1
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3
4
2
3
3
3
	
2
1
2
3
1
0
3
3
4
1
3
3
3

In [156]:

    

goSims <- matrix(numeric(), nrow=numCom, ncol=numCom)

for (i in 1:numCom){
    for (j in 1:numCom){
        goSims[i, j] = mgoSim(names(gos[[i]]), names(gos[[j]]), measure="Wang", semData=scGO, combine="BMA")
    }
}


    

In [157]:

    

head(goSims)


    

    







	
1.000
0.164
0.093
0.140
0.602
0.145
0.221
0.338
0.134
0.276
NA   
0.525
0.626
	
0.164
1.000
0.633
0.475
0.171
0.348
0.363
0.322
0.672
0.234
NA   
0.362
0.082
	
0.093
0.633
1.000
0.343
0.085
0.286
0.411
0.201
0.563
0.200
NA   
0.246
0.073
	
0.140
0.475
0.343
1.000
0.132
0.321
0.236
0.226
1.000
0.276
NA   
0.331
0.094
	
0.602
0.171
0.085
0.132
1.000
0.182
0.298
0.511
0.134
0.234
NA   
0.447
0.537
	
0.145
0.348
0.286
0.321
0.182
1.000
0.285
0.278
0.385
0.286
NA   
0.368
0.137

In [18]:

    

wangGoSims <- sapply(names(enrichedGOs), 
                     function(i) sapply(names(enrichedGOs), 
                                        function(j) mgoSim(i, j, semData=scGO, measure="Wang", combine="BMA")))


    

In [19]:

    

wangGoSims


    

In [22]:

    

mgeneSim(allGeneNames[as.integer(g[[1]])], semData=scGO, measure="Wang", combine="BMA")


    

    




  |======================================================================| 100%






    






YML028W
YGL122C
YPL214C
YHL006C
YKL130C
YCR011C
YBL007C
YJR091C
YGL145W
YBR133C
YDR214W
YGR268C
YLR291C
YOR138C
YEL023C
YFR002W

	
YML028W
1.000
0.218
0.330
0.389
0.193
0.385
0.183
0.150
0.121
0.324
0.547
0.477
0.146
0.157
0.477
0.152
	
YGL122C
0.218
1.000
0.270
0.318
0.119
0.340
0.085
0.332
0.451
0.351
0.098
0.185
0.295
0.223
0.185
0.326
	
YPL214C
0.330
0.270
1.000
0.338
0.188
0.171
0.131
0.212
0.053
0.319
0.106
0.069
0.396
0.123
0.069
0.080
	
YHL006C
0.389
0.318
0.338
1.000
0.208
0.234
0.264
0.263
0.078
0.310
0.235
0.105
0.230
0.249
0.105
0.196
	
YKL130C
0.193
0.119
0.188
0.208
1.000
0.245
0.176
0.298
0.203
0.152
0.142
0.243
0.118
0.091
0.243
0.156
	
YCR011C
0.385
0.340
0.171
0.234
0.245
1.000
0.391
0.242
0.512
0.373
0.284
0.196
0.161
0.112
0.196
0.350
	
YBL007C
0.183
0.085
0.131
0.264
0.176
0.391
1.000
0.149
0.453
0.167
0.158
0.283
0.079
0.062
0.283
0.328
	
YJR091C
0.150
0.332
0.212
0.263
0.298
0.242
0.149
1.000
0.344
0.210
0.118
0.200
0.115
0.140
0.200
0.221
	
YGL145W
0.121
0.451
0.053
0.078
0.203
0.512
0.453
0.344
1.000
0.117
0.095
0.158
0.045
0.035
0.158
0.451
	
YBR133C
0.324
0.351
0.319
0.310
0.152
0.373
0.167
0.210
0.117
1.000
0.192
0.217
0.294
0.330
0.217
0.132
	
YDR214W
0.547
0.098
0.106
0.235
0.142
0.284
0.158
0.118
0.095
0.192
1.000
0.477
0.099
0.144
0.477
0.145
	
YGR268C
0.477
0.185
0.069
0.105
0.243
0.196
0.283
0.200
0.158
0.217
0.477
1.000
0.077
0.144
1.000
0.203
	
YLR291C
0.146
0.295
0.396
0.230
0.118
0.161
0.079
0.115
0.045
0.294
0.099
0.077
1.000
0.268
0.077
0.064
	
YOR138C
0.157
0.223
0.123
0.249
0.091
0.112
0.062
0.140
0.035
0.330
0.144
0.144
0.268
1.000
0.144
0.070
	
YEL023C
0.477
0.185
0.069
0.105
0.243
0.196
0.283
0.200
0.158
0.217
0.477
1.000
0.077
0.144
1.000
0.203
	
YFR002W
0.152
0.326
0.080
0.196
0.156
0.350
0.328
0.221
0.451
0.132
0.145
0.203
0.064
0.070
0.203
1.000

In [21]:

    

mgoSim(names(enrichedGOs[[1]]), names(enrichedGOs[[2]]), semData=scGO, measure="Wang", combine="BMA")


    

    





0.106

In [15]:

    

head(shortest.path)


    

    






V1
V2
V3
V4
V5
V6

	
0
1
1
1
1
1
	
1
0
1
2
2
2
	
1
1
0
1
1
1
	
1
2
1
0
2
2
	
1
2
1
2
0
2
	
1
2
1
2
2
0

In [116]:

    

distances <- numeric(length = (numCom * (numCom - 1)) / 2)
semSims <- numeric(length = (numCom * (numCom - 1)) / 2)

completed <- 0

for (c1 in 1:length(enrichedGOsPathway)) {
    
    for (c2 in c1:length(enrichedGOsPathway)) {
        
        if (c1 == c2) next   
        
        completed <- completed + 1  
        semSims[completed] <- simsPathway[c1, c2]
            
        distances[completed] <- shortest.path[c1, c2]
        
        print(sprintf("Completed: %s", completed))
    }
}


    

    




[1] "Completed: 1"
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In [117]:

    

plot(distances, semSims, xlab="Distance on Map", ylab="Shared Paths")


    

In [102]:

    

cor(distances, semSims, method="spearman")


    

    





-0.05678168738453

In [42]:

    

library(GOSim)
setOntology(ont, loadIC=FALSE)
setEvidenceLevel(evidences="all",organism=org.Sc.sgdORGANISM, gomap=org.Sc.sgdGO)
e <- GOenrichment(g[[46]], allGenes)


    

    




-> retrieving GO information for all available genes for organism 'Saccharomyces cerevisiae' in GO database
-> filtering GO terms according to evidence levels 'all'

Building most specific GOs .....
	( 1690 GO terms found. )

Build GO DAG topology ..........
	( 3645 GO terms and 8243 relations. )

Annotating nodes ...............
	( 1567 genes annotated to the GO terms. )

			 -- Elim Algorithm -- 

		 the algorithm is scoring 172 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

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

	 Level 11:	9 nodes to be scored	(0 eliminated genes)

	 Level 10:	8 nodes to be scored	(1 eliminated genes)

	 Level 9:	17 nodes to be scored	(3 eliminated genes)

	 Level 8:	14 nodes to be scored	(8 eliminated genes)

	 Level 7:	20 nodes to be scored	(8 eliminated genes)

	 Level 6:	25 nodes to be scored	(8 eliminated genes)

	 Level 5:	28 nodes to be scored	(8 eliminated genes)

	 Level 4:	20 nodes to be scored	(28 eliminated genes)

	 Level 3:	12 nodes to be scored	(28 eliminated genes)

	 Level 2:	7 nodes to be scored	(28 eliminated genes)

	 Level 1:	1 nodes to be scored	(28 eliminated genes)

In [49]:

    

e


    

    






	
$GOTerms
		

go_id
Term
Definition

	
15591
GO:0018343                                                                                                 
protein farnesylation                                                                                      
The covalent attachment of a farnesyl group to a protein.                                                  
	
15594
GO:0018344                                                                                                 
protein geranylgeranylation                                                                                
The covalent attachment of a geranylgeranyl group to a protein.                                            
	
16626
GO:0006874                                                                                                 
cellular calcium ion homeostasis                                                                           
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
	
17047
GO:0030010                                                                                                 
establishment of cell polarity                                                                             
The specification and formation of anisotropic intracellular organization or cell growth patterns.         
	
48636
GO:0042127                                                                                                 
regulation of cell proliferation                                                                           
Any process that modulates the frequency, rate or extent of cell proliferation.                            
	
79331
GO:0070884                                                                                                 
regulation of calcineurin-NFAT signaling cascade                                                           
Any process that modulates the frequency, rate or extent of the calcineurin-NFAT signaling cascade.        



	
$p.values
		

	
GO:0006874
		
0.00891715384596614
	
GO:0042127
		
0.00446713465220172
	
GO:0070884
		
0.00446713465220172
	
GO:0018343
		
1.71154584375543e-05
	
GO:0018344
		
0.000170063041559058
	
GO:0030010
		
0.00345128149568176


	
$genes
		

	
$`GO:0006874`
		

	
'YBR187W'
	
'YGL155W'


	
$`GO:0042127`
		
'YDL090C'
	
$`GO:0070884`
		
'YKL159C'
	
$`GO:0018343`
		

	
'YDL090C'
	
'YKL019W'


	
$`GO:0018344`
		

	
'YGL155W'
	
'YJL031C'
	
'YKL019W'
	
'YOR370C'
	
'YPR176C'


	
$`GO:0030010`
		

	
'YCR063W'
	
'YER093C'
	
'YER118C'
	
'YER149C'
	
'YFL039C'
	
'YGL054C'
	
'YGL155W'
	
'YGR014W'
	
'YGR058W'
	
'YGR262C'
	
'YHR115C'
	
'YHR129C'
	
'YIL144W'
	
'YLL049W'
	
'YLR319C'
	
'YMR294W'
	
'YNL116W'
	
'YOR127W'
	
'YOR301W'
	
'YPL161C'
	
'YPL174C'

In [88]:

    

goTerms <- e$GOTerms
p.values <- e$p.values


    

In [89]:

    

p.values.df <- data.frame(p.values)
p.values.df["go_id"] <- names(p.values)
p.values.df


    

    






p.values
go_id

	
GO:0006874
8.917154e-03
GO:0006874  
	
GO:0042127
4.467135e-03
GO:0042127  
	
GO:0070884
4.467135e-03
GO:0070884  
	
GO:0018343
1.711546e-05
GO:0018343  
	
GO:0018344
1.700630e-04
GO:0018344  
	
GO:0030010
3.451281e-03
GO:0030010  

In [90]:

    

goTerms <- merge(goTerms, p.values.df, by="go_id")


    

In [93]:

    

colnames(goTerms) <- c("GO_ID", "TERM", "DEFINITION", "P_VALUE")
head(goTerms)


    

    






GO_ID
TERM
DEFINITION
P_VALUE

	
GO:0006874                                                                                                 
cellular calcium ion homeostasis                                                                           
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
8.917154e-03                                                                                               
	
GO:0018343                                                                                                 
protein farnesylation                                                                                      
The covalent attachment of a farnesyl group to a protein.                                                  
1.711546e-05                                                                                               
	
GO:0018344                                                                                                 
protein geranylgeranylation                                                                                
The covalent attachment of a geranylgeranyl group to a protein.                                            
1.700630e-04                                                                                               
	
GO:0030010                                                                                                 
establishment of cell polarity                                                                             
The specification and formation of anisotropic intracellular organization or cell growth patterns.         
3.451281e-03                                                                                               
	
GO:0042127                                                                                                 
regulation of cell proliferation                                                                           
Any process that modulates the frequency, rate or extent of cell proliferation.                            
4.467135e-03                                                                                               
	
GO:0070884                                                                                                 
regulation of calcineurin-NFAT signaling cascade                                                           
Any process that modulates the frequency, rate or extent of the calcineurin-NFAT signaling cascade.        
4.467135e-03                                                                                               

In [94]:

    

library(gridExtra)
grid.table(goTerms[,c("GO_ID", "TERM", "P_VALUE")])


    

In [46]:

    

g[[46]]


    

    






	
'YKL019W'
	
'YGL155W'
	
'YKL159C'
	
'YCR063W'
	
'YBR247C'
	
'YDL090C'
	
'YOL135C'

In [103]:

    

l <- as.list(org.Sc.sgdGO[["YKL019W"]])


    

In [116]:

    

gos <- sapply(l, function(i) i[["GOID"]])


    

In [122]:

    

t <- select(GO.db, keys=gos, columns=c("GOID","TERM","ONTOLOGY"))


    

    




'select()' returned many:1 mapping between keys and columns

In [123]:

    

grid.table(t)


    

In [ ]: