notebook.community

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In [1]:

    
library(GO.db)
library(topGO)
library(org.Sc.sgd.db)









    



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



In [1]:

    
setwd('/home/david/Documents/ghsom')
allGenes <- read.table("Y2H_union.txt")$V1
allGenes <- unique(allGenes)
length(allGenes)



In [3]:

    
setwd('/home/david/Documents/ghsom')
myInterestingGenes <- read.table("community_one.txt")$V1
myInterestingGenes









    





	YJR058C
	YHR105W
	YBR135W
	YBR160W
	YNL037C
	YGL156W
	YJL138C
	YBR254C
	YLR102C
	YOR379C
	YIR018W
	YOR136W
	YPL128C
	YKR059W
	YHR112C
	YPL280W
	YML042W
	YDR421W
	YOR155C
	YHR113W
	YNL044W
	YLR021W
	YJR021C
	YLR347C
	YFL010C
	YMR096W
	YDL164C
	YDR027C
	YML108W
	YGL015C
	YLR442C
	YNL098C
	YFL059W
	YDL066W
	YFL017WA
	YCL033C
	YIL053W
	YBR176W
	YMR322C
	YER062C
	YMR276W
	YPL201C
	YKL090W
	YDR256C
	YPL091W
	YLR245C
	YMR218C
	YDR122W
	YGL213C
	YMR308C
	YOR097C
	YGL071W
	YGR024C
	YHR156C
	YNL334C
	YNL316C
	YPL088W
	YGL037C
	YKL103C
	YBL037W
	YGL175C
	YIL119C
	YLR315W
	YOL145C
	YHL009C
	YNL222W
	YDR189W
	YGR108W
	YKR068C
	YFL039C
	YGR144W
	YIL051C
	YPL125W
	YGL187C
	YDR244W
	YJR052W
	YBR107C
	YPR054W
	YPR049C
	YDR502C
	YBL057C
	YPR062W
	YHR039C
	YOR391C
	YDR480W
	YMR033W
	YJR112W
	YBR252W
	YGR058W
	YPR193C
	YOR115C
	YPL110C
	YGR267C
	YOL082W
	YNL138W
	YDR472W
	YGR179C
	YPL251W
	YFL029C
	YJL199C
	YML077W
	YMR092C
	YIL082W
	YPR160W
	YLR377C
	YNL107W
	YOR380W
	YFL060C
	YJL104W
	YJL103C
	YHL018W
	YOR095C
	YOL054W
	YDR518W
	YLR319C
	YNL153C
	YJR010W
	YLR026C
	YMR095C



In [5]:

    
geneList <- factor(as.integer(allGenes %in% myInterestingGenes))
# names(geneList) <- ensembl2GO[allGenes]
# names(geneList) <- ensembl2ORF[allGenes]
names(geneList) <- allGenes
geneList









    





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In [6]:

    
GOdata <- new("topGOdata", description="Practice GOData object UNION", ontology = "BP", allGenes = geneList,
              annotationFun = annFUN.org, mapping = "org.Sc.sgd.db", ID = "ENSEMBL", nodeSize = 10)
GOdata









    



Building most specific GOs .....
	( 1567 GO terms found. )

Build GO DAG topology ..........
	( 3506 GO terms and 7914 relations. )

Annotating nodes ...............
	( 1276 genes annotated to the GO terms. )






    





------------------------- topGOdata object -------------------------

 Description:
   -  Practice GOData object UNION 

 Ontology:
   -  BP 

 1337 available genes (all genes from the array):
   - symbol:  MEL1 Q0085 TORF1 TORF19 TORF21  ...
   - 83  significant genes. 

 1276 feasible genes (genes that can be used in the analysis):
   - symbol:  Q0085 YAL005C YAL012W YAL016W YAL020C  ...
   - 81  significant genes. 

 GO graph (nodes with at least  10  genes):
   - a graph with directed edges
   - number of nodes = 874 
   - number of edges = 1832 

------------------------- topGOdata object -------------------------



In [7]:

    
resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
resultFisher









    



			 -- Classic Algorithm -- 

		 the algorithm is scoring 613 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    





Description: Practice GOData object UNION 
Ontology: BP 
'classic' algorithm with the 'fisher' test
874 GO terms scored: 21 terms with p < 0.01
Annotation data:
    Annotated genes: 1276 
    Significant genes: 81 
    Min. no. of genes annotated to a GO: 10 
    Nontrivial nodes: 613



In [8]:

    
resultFisher.elim <- runTest(GOdata, algorithm = "elim", statistic = "fisher")
resultFisher.elim









    



			 -- Elim Algorithm -- 

		 the algorithm is scoring 613 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

	 Level 13:	6 nodes to be scored	(0 eliminated genes)

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

	 Level 11:	17 nodes to be scored	(0 eliminated genes)

	 Level 10:	30 nodes to be scored	(0 eliminated genes)

	 Level 9:	56 nodes to be scored	(0 eliminated genes)

	 Level 8:	67 nodes to be scored	(0 eliminated genes)

	 Level 7:	79 nodes to be scored	(0 eliminated genes)

	 Level 6:	105 nodes to be scored	(53 eliminated genes)

	 Level 5:	115 nodes to be scored	(91 eliminated genes)

	 Level 4:	80 nodes to be scored	(108 eliminated genes)

	 Level 3:	34 nodes to be scored	(256 eliminated genes)

	 Level 2:	12 nodes to be scored	(256 eliminated genes)

	 Level 1:	1 nodes to be scored	(256 eliminated genes)






    





Description: Practice GOData object UNION 
Ontology: BP 
'elim' algorithm with the 'fisher : 0.01' test
874 GO terms scored: 9 terms with p < 0.01
Annotation data:
    Annotated genes: 1276 
    Significant genes: 81 
    Min. no. of genes annotated to a GO: 10 
    Nontrivial nodes: 613



In [9]:

    
allRes <- GenTable(GOdata, classicFisher = resultFisher,
                   elimFisher = resultFisher.elim,
                   orderBy = "classicFisher", ranksOf = "elimFisher", topNodes = 10)
allRes









    





GO.ID Term Annotated Significant Expected Rank in elimFisher classicFisher elimFisher

	GO:0009110                                 vitamin biosynthetic process                19                                         8                                          1.21                                      607                                        8.0e-06                                    1.0000                                     
	GO:0042364                                 water-soluble vitamin biosynthetic proce...  19                                         8                                          1.21                                        1                                        8.0e-06                                    8.0e-06                                    
	GO:0072525                                 pyridine-containing compound biosyntheti...  16                                         7                                          1.02                                        2                                        2.3e-05                                    2.3e-05                                    
	GO:0006766                                 vitamin metabolic process                   23                                         8                                          1.46                                      608                                        4.2e-05                                    1.0000                                     
	GO:0006767                                 water-soluble vitamin metabolic process     23                                         8                                          1.46                                      609                                        4.2e-05                                    1.0000                                     
	GO:0072528                                 pyrimidine-containing compound biosynthe...  18                                         7                                          1.14                                        3                                        5.8e-05                                    5.8e-05                                    
	GO:0044281                                 small molecule metabolic process           218                                        28                                         13.84                                        8                                        6.2e-05                                    0.0066                                     
	GO:0044272                                 sulfur compound biosynthetic process        13                                         6                                          0.83                                        4                                        6.5e-05                                    6.5e-05                                    
	GO:0072527                                 pyrimidine-containing compound metabolic...  20                                         7                                          1.27                                      610                                        0.00013                                    1.0000                                     
	GO:0009108                                 coenzyme biosynthetic process               35                                         9                                          2.22                                        5                                        0.00020                                    0.0002



In [10]:

    
showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo ='all')









    



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







    





$dag
A graphNEL graph with directed edges
Number of Nodes = 29 
Number of Edges = 52 

$complete.dag
[1] "A graph with 29 nodes."



In [11]:

    
graph(GOdata)









    





A graphNEL graph with directed edges
Number of Nodes = 874 
Number of Edges = 1832



In [4]:

    
setwd('/home/david/Documents/ghsom')
myInterestingGenes2 <- read.table("community_two.txt")$V1
myInterestingGenes2









    





	YJL155C
	YNR046W
	YBR190W
	YDL238C
	YBL051C
	YLR257W
	YJR047C
	YIL151C
	YIR015W
	YLR322W
	YJR046W
	YBL101WA
	YDR488C
	YLR121C
	YLR465C
	YLR321C
	YIR037W
	YHR129C
	YLR345W
	YJL162C
	YLR216C
	YLR389C
	YBR221C
	YDR106W
	YML035C
	YEL034W
	YJL070C
	YMR168C
	YBR111C
	YKR096W
	YIL132C
	YLR376C
	YLR117C
	YDR504C
	YHR068W
	YDL111C
	YBR175W
	YBR284W
	YBR244W
	YAR003W
	YDR140W
	YJR008W
	YDR424C
	YGR158C
	YPL070W



In [12]:

    
geneList2 <- factor(as.integer(allGenes %in% myInterestingGenes2))
# names(geneList) <- ensembl2GO[allGenes]
# names(geneList) <- ensembl2ORF[allGenes]
names(geneList2) <- allGenes
geneList2









    





	MEL1
		0
	Q0085
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	TORF1
		0
	TORF19
		0
	TORF21
		0
	TORF47
		0
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		0
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		0
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		0
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		0
	YAL021C
		0
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		0
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		0
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		0
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		0
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		0
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		0
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		0
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		0
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		0
	YAL060W
		0
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		0
	YAR003W
		1
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		0
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		0
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		0
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		0
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		0
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		0
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		0
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		0
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		0
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In [13]:

    
GOdata2 <- new("topGOdata", description="Practice GOData object UNION", ontology = "BP", allGenes = geneList2,
              annotationFun = annFUN.org, mapping = "org.Sc.sgd.db", ID = "ENSEMBL", nodeSize = 10)
GOdata2









    



Building most specific GOs .....
	( 1567 GO terms found. )

Build GO DAG topology ..........
	( 3506 GO terms and 7914 relations. )

Annotating nodes ...............
	( 1276 genes annotated to the GO terms. )






    





------------------------- topGOdata object -------------------------

 Description:
   -  Practice GOData object UNION 

 Ontology:
   -  BP 

 1337 available genes (all genes from the array):
   - symbol:  MEL1 Q0085 TORF1 TORF19 TORF21  ...
   - 33  significant genes. 

 1276 feasible genes (genes that can be used in the analysis):
   - symbol:  Q0085 YAL005C YAL012W YAL016W YAL020C  ...
   - 30  significant genes. 

 GO graph (nodes with at least  10  genes):
   - a graph with directed edges
   - number of nodes = 874 
   - number of edges = 1832 

------------------------- topGOdata object -------------------------



In [14]:

    
resultFisher2 <- runTest(GOdata2, algorithm = "classic", statistic = "fisher")
resultFisher2









    



			 -- Classic Algorithm -- 

		 the algorithm is scoring 435 nontrivial nodes
		 parameters: 
			 test statistic: fisher






    





Description: Practice GOData object UNION 
Ontology: BP 
'classic' algorithm with the 'fisher' test
874 GO terms scored: 8 terms with p < 0.01
Annotation data:
    Annotated genes: 1276 
    Significant genes: 30 
    Min. no. of genes annotated to a GO: 10 
    Nontrivial nodes: 435



In [16]:

    
resultFisher2.elim <- runTest(GOdata2, algorithm = "elim", statistic = "fisher")
resultFisher2.elim









    



			 -- Elim Algorithm -- 

		 the algorithm is scoring 435 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

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

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

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

	 Level 11:	17 nodes to be scored	(0 eliminated genes)

	 Level 10:	28 nodes to be scored	(0 eliminated genes)

	 Level 9:	43 nodes to be scored	(11 eliminated genes)

	 Level 8:	49 nodes to be scored	(11 eliminated genes)

	 Level 7:	50 nodes to be scored	(21 eliminated genes)

	 Level 6:	77 nodes to be scored	(27 eliminated genes)

	 Level 5:	76 nodes to be scored	(27 eliminated genes)

	 Level 4:	52 nodes to be scored	(27 eliminated genes)

	 Level 3:	24 nodes to be scored	(27 eliminated genes)

	 Level 2:	9 nodes to be scored	(27 eliminated genes)

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






    





Description: Practice GOData object UNION 
Ontology: BP 
'elim' algorithm with the 'fisher : 0.01' test
874 GO terms scored: 3 terms with p < 0.01
Annotation data:
    Annotated genes: 1276 
    Significant genes: 30 
    Min. no. of genes annotated to a GO: 10 
    Nontrivial nodes: 435



In [17]:

    
allRes2 <- GenTable(GOdata2, classicFisher = resultFisher,
                   elimFisher = resultFisher.elim,
                   orderBy = "classicFisher", ranksOf = "elimFisher", topNodes = 10)
allRes2









    





GO.ID Term Annotated Significant Expected Rank in elimFisher classicFisher elimFisher

	GO:0009110                                 vitamin biosynthetic process                19                                        0                                          0.45                                       607                                        8.0e-06                                    1.0000                                     
	GO:0042364                                 water-soluble vitamin biosynthetic proce...  19                                        0                                          0.45                                         1                                        8.0e-06                                    8.0e-06                                    
	GO:0072525                                 pyridine-containing compound biosyntheti...  16                                        0                                          0.38                                         2                                        2.3e-05                                    2.3e-05                                    
	GO:0006766                                 vitamin metabolic process                   23                                        0                                          0.54                                       608                                        4.2e-05                                    1.0000                                     
	GO:0006767                                 water-soluble vitamin metabolic process     23                                        0                                          0.54                                       609                                        4.2e-05                                    1.0000                                     
	GO:0072528                                 pyrimidine-containing compound biosynthe...  18                                        0                                          0.42                                         3                                        5.8e-05                                    5.8e-05                                    
	GO:0044281                                 small molecule metabolic process           218                                        5                                          5.13                                         8                                        6.2e-05                                    0.0066                                     
	GO:0044272                                 sulfur compound biosynthetic process        13                                        1                                          0.31                                         4                                        6.5e-05                                    6.5e-05                                    
	GO:0072527                                 pyrimidine-containing compound metabolic...  20                                        0                                          0.47                                       610                                        0.00013                                    1.0000                                     
	GO:0009108                                 coenzyme biosynthetic process               35                                        1                                          0.82                                         5                                        0.00020                                    0.0002



In [18]:

    
showSigOfNodes(GOdata2, score(resultFisher2), firstSigNodes = 5, useInfo ='all')









    





$dag
A graphNEL graph with directed edges
Number of Nodes = 29 
Number of Edges = 48 

$complete.dag
[1] "A graph with 29 nodes."



In [22]:

    
printGraph(GOdata, resultFisher, firstSigNodes = 5, fn.prefix = "tGO", useInfo = "all", pdfSW = TRUE)









    



tGO_classic_5_all  --- no of nodes:  29



In [21]:

    
printGraph(GOdata2, resultFisher2, firstSigNodes = 5, fn.prefix = "tGO", useInfo = "all", pdfSW = TRUE)









    



tGO_classic_5_all  --- no of nodes:  29



In [40]:

    
g1 <- names(score(resultFisher)[score(resultFisher) < 0.05])
g2 <- names(score(resultFisher2)[score(resultFisher2) < 0.05])



In [24]:

    
source("https://bioconductor.org/biocLite.R")
biocLite("GOSemSim")









    



Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘GOSemSim’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'backports', 'broom', 'colorspace', 'data.table', 'digest',
  'forcats', 'ggplot2', 'jsonlite', 'Matrix', 'mgcv', 'nlme', 'openssl',
  'pbdZMQ', 'psych', 'Rcpp', 'rprojroot', 'selectr', 'shiny', 'stringr',
  'tidyr', 'tidyverse', 'xml2', 'zoo'



In [26]:

    
library(GOSemSim)
scGO <- godata('org.Sc.sgd.db', ont="BP")









    



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



In [49]:

    
semSim <- mgoSim(g1, g2, semData=scGO, measure="Wang", combine=NULL)
mean(semSim)



In [51]:

    
semSim









    





GO:0000184 GO:0000469 GO:0000724 GO:0000725 GO:0000731 GO:0006090 GO:0006163 GO:0006165 GO:0006275 GO:0006301 ⋯ GO:0043144 GO:0043628 GO:0044786 GO:0045003 GO:0046939 GO:0051293 GO:0051345 GO:0051647 GO:0051653 GO:0071824

	GO:0006081 0.252 0.269 0.463 0.483 0.372 0.627 0.445 0.451 0.206 0.503 ⋯    0.300 0.300 0.445 0.465 0.480 0.215 0.137 0.092 0.325 0.197
	GO:0006082 0.243 0.261 0.439 0.460 0.356 0.776 0.483 0.490 0.200 0.479 ⋯    0.288 0.288 0.424 0.440 0.521 0.208 0.131 0.087 0.311 0.186
	GO:0006732 0.196 0.213 0.218 0.229 0.170 0.320 0.218 0.210 0.155 0.240 ⋯    0.242 0.242 0.208 0.220 0.230 0.100 0.150 0.113 0.159 0.238
	GO:0006766 0.087 0.095 0.229 0.242 0.174 0.428 0.273 0.287 0.072 0.254 ⋯    0.108 0.108 0.232 0.230 0.306 0.100 0.150 0.113 0.159 0.106
	GO:0006767 0.074 0.082 0.201 0.215 0.152 0.361 0.236 0.247 0.063 0.226 ⋯    0.092 0.092 0.207 0.199 0.263 0.088 0.131 0.099 0.140 0.092
	GO:0006790 0.236 0.250 0.254 0.263 0.198 0.384 0.252 0.248 0.181 0.277 ⋯    0.289 0.289 0.241 0.260 0.270 0.115 0.174 0.133 0.183 0.278
	GO:0006887 0.066 0.072 0.176 0.188 0.141 0.213 0.161 0.164 0.056 0.195 ⋯    0.078 0.078 0.169 0.172 0.172 0.407 0.047 0.227 0.431 0.145
	GO:0006888 0.022 0.026 0.065 0.071 0.051 0.076 0.058 0.059 0.021 0.074 ⋯    0.028 0.028 0.068 0.062 0.062 0.292 0.039 0.215 0.274 0.056
	GO:0007568 0.047 0.049 0.118 0.123 0.090 0.171 0.107 0.112 0.037 0.129 ⋯    0.057 0.057 0.118 0.120 0.120 0.115 0.077 0.133 0.183 0.123
	GO:0009064 0.218 0.242 0.342 0.371 0.288 0.583 0.435 0.368 0.192 0.386 ⋯    0.258 0.258 0.333 0.330 0.391 0.129 0.100 0.067 0.200 0.126
	GO:0009108 0.147 0.165 0.170 0.181 0.226 0.227 0.172 0.162 0.205 0.189 ⋯    0.180 0.180 0.274 0.167 0.176 0.079 0.112 0.078 0.120 0.167
	GO:0009110 0.153 0.168 0.326 0.346 0.355 0.460 0.351 0.355 0.213 0.358 ⋯    0.181 0.181 0.486 0.321 0.375 0.187 0.106 0.071 0.269 0.154
	GO:0022413 0.056 0.058 0.061 0.063 0.046 0.090 0.058 0.058 0.043 0.066 ⋯    0.068 0.068 0.060 0.062 0.062 0.061 0.089 0.153 0.093 0.142
	GO:0032505 0.060 0.062 0.065 0.067 0.049 0.102 0.062 0.063 0.046 0.071 ⋯    0.074 0.074 0.064 0.068 0.067 0.066 0.099 0.181 0.103 0.166
	GO:0032940 0.078 0.085 0.204 0.215 0.163 0.253 0.187 0.192 0.065 0.223 ⋯    0.093 0.093 0.195 0.202 0.202 0.464 0.054 0.259 0.490 0.168
	GO:0042364 0.132 0.147 0.289 0.310 0.314 0.400 0.310 0.311 0.186 0.321 ⋯    0.157 0.157 0.435 0.281 0.329 0.166 0.095 0.064 0.241 0.138
	GO:0043094 0.188 0.205 0.210 0.221 0.275 0.300 0.210 0.202 0.250 0.231 ⋯    0.231 0.231 0.335 0.211 0.220 0.096 0.142 0.104 0.150 0.220
	GO:0044272 0.179 0.195 0.200 0.211 0.265 0.279 0.201 0.193 0.242 0.221 ⋯    0.218 0.218 0.321 0.200 0.209 0.092 0.133 0.094 0.141 0.201
	GO:0044281 0.105 0.111 0.266 0.277 0.201 0.516 0.320 0.339 0.084 0.291 ⋯    0.128 0.128 0.266 0.270 0.361 0.115 0.174 0.133 0.183 0.123
	GO:0044283 0.080 0.087 0.211 0.223 0.210 0.373 0.251 0.263 0.111 0.234 ⋯    0.097 0.097 0.364 0.210 0.279 0.092 0.133 0.094 0.141 0.089
	GO:0044702 0.055 0.057 0.135 0.139 0.103 0.198 0.123 0.130 0.043 0.146 ⋯    0.066 0.066 0.133 0.139 0.138 0.131 0.088 0.148 0.206 0.138
	GO:0044710 0.128 0.132 0.313 0.322 0.237 0.462 0.280 0.296 0.099 0.339 ⋯    0.155 0.155 0.309 0.323 0.316 0.134 0.206 0.159 0.215 0.148
	GO:0044711 0.099 0.106 0.253 0.265 0.250 0.348 0.225 0.235 0.133 0.277 ⋯    0.121 0.121 0.430 0.256 0.250 0.110 0.162 0.119 0.171 0.111
	GO:0046903 0.036 0.039 0.095 0.101 0.073 0.127 0.086 0.089 0.030 0.105 ⋯    0.044 0.044 0.097 0.095 0.095 0.273 0.060 0.220 0.325 0.092
	GO:0046907 0.037 0.040 0.043 0.046 0.033 0.059 0.041 0.041 0.031 0.048 ⋯    0.045 0.045 0.044 0.043 0.043 0.312 0.062 0.370 0.239 0.096
	GO:0048193 0.027 0.030 0.074 0.080 0.058 0.090 0.067 0.068 0.024 0.083 ⋯    0.032 0.032 0.077 0.072 0.072 0.321 0.045 0.240 0.307 0.065
	GO:0051186 0.236 0.250 0.254 0.263 0.198 0.384 0.252 0.248 0.181 0.277 ⋯    0.289 0.289 0.241 0.260 0.270 0.115 0.174 0.133 0.183 0.278
	GO:0051188 0.179 0.195 0.200 0.211 0.265 0.279 0.201 0.193 0.242 0.221 ⋯    0.218 0.218 0.321 0.200 0.209 0.092 0.133 0.094 0.141 0.201
	GO:0051321 0.080 0.087 0.212 0.224 0.166 0.277 0.193 0.200 0.065 0.234 ⋯    0.096 0.096 0.272 0.211 0.211 0.264 0.061 0.094 0.406 0.192
	GO:0055086 0.458 0.482 0.609 0.639 0.546 0.478 0.782 0.741 0.395 0.661 ⋯    0.514 0.514 0.585 0.604 0.777 0.176 0.098 0.064 0.248 0.139
	GO:0072524 0.421 0.440 0.425 0.441 0.372 0.304 0.566 0.445 0.347 0.459 ⋯    0.485 0.485 0.402 0.430 0.472 0.082 0.113 0.075 0.120 0.161
	GO:0072525 0.289 0.311 0.300 0.317 0.518 0.198 0.414 0.313 0.356 0.328 ⋯    0.327 0.327 0.410 0.296 0.330 0.061 0.078 0.048 0.084 0.104
	GO:0072527 0.421 0.440 0.425 0.441 0.372 0.304 0.566 0.445 0.347 0.459 ⋯    0.485 0.485 0.402 0.430 0.472 0.082 0.113 0.075 0.120 0.161
	GO:0072528 0.289 0.311 0.300 0.317 0.518 0.198 0.414 0.313 0.356 0.328 ⋯    0.327 0.327 0.410 0.296 0.330 0.061 0.078 0.048 0.084 0.104
	GO:1901564 0.240 0.248 0.245 0.251 0.198 0.284 0.361 0.256 0.190 0.263 ⋯    0.287 0.287 0.234 0.254 0.273 0.053 0.171 0.130 0.080 0.121
	GO:1901566 0.182 0.193 0.191 0.199 0.259 0.208 0.289 0.200 0.245 0.208 ⋯    0.216 0.216 0.309 0.194 0.211 0.043 0.132 0.093 0.062 0.088
	GO:1901615 0.182 0.191 0.192 0.198 0.149 0.310 0.197 0.199 0.142 0.208 ⋯    0.222 0.222 0.185 0.198 0.212 0.056 0.184 0.146 0.086 0.135
	GO:1901617 0.136 0.147 0.149 0.156 0.222 0.220 0.155 0.153 0.208 0.163 ⋯    0.164 0.164 0.274 0.150 0.163 0.045 0.138 0.100 0.065 0.094
	GO:1903046 0.066 0.074 0.195 0.208 0.153 0.248 0.177 0.183 0.056 0.216 ⋯    0.080 0.080 0.316 0.193 0.193 0.301 0.045 0.069 0.463 0.162



In [ ]:

GO.ID	Term	Annotated	Significant	Expected	Rank in elimFisher	classicFisher	elimFisher
GO:0009110	vitamin biosynthetic process	19	8	1.21	607	8.0e-06	1.0000
GO:0042364	water-soluble vitamin biosynthetic proce...	19	8	1.21	1	8.0e-06	8.0e-06
GO:0072525	pyridine-containing compound biosyntheti...	16	7	1.02	2	2.3e-05	2.3e-05
GO:0006766	vitamin metabolic process	23	8	1.46	608	4.2e-05	1.0000
GO:0006767	water-soluble vitamin metabolic process	23	8	1.46	609	4.2e-05	1.0000
GO:0072528	pyrimidine-containing compound biosynthe...	18	7	1.14	3	5.8e-05	5.8e-05
GO:0044281	small molecule metabolic process	218	28	13.84	8	6.2e-05	0.0066
GO:0044272	sulfur compound biosynthetic process	13	6	0.83	4	6.5e-05	6.5e-05
GO:0072527	pyrimidine-containing compound metabolic...	20	7	1.27	610	0.00013	1.0000
GO:0009108	coenzyme biosynthetic process	35	9	2.22	5	0.00020	0.0002

GO.ID	Term	Annotated	Significant	Expected	Rank in elimFisher	classicFisher	elimFisher
GO:0009110	vitamin biosynthetic process	19	0	0.45	607	8.0e-06	1.0000
GO:0042364	water-soluble vitamin biosynthetic proce...	19	0	0.45	1	8.0e-06	8.0e-06
GO:0072525	pyridine-containing compound biosyntheti...	16	0	0.38	2	2.3e-05	2.3e-05
GO:0006766	vitamin metabolic process	23	0	0.54	608	4.2e-05	1.0000
GO:0006767	water-soluble vitamin metabolic process	23	0	0.54	609	4.2e-05	1.0000
GO:0072528	pyrimidine-containing compound biosynthe...	18	0	0.42	3	5.8e-05	5.8e-05
GO:0044281	small molecule metabolic process	218	5	5.13	8	6.2e-05	0.0066
GO:0044272	sulfur compound biosynthetic process	13	1	0.31	4	6.5e-05	6.5e-05
GO:0072527	pyrimidine-containing compound metabolic...	20	0	0.47	610	0.00013	1.0000
GO:0009108	coenzyme biosynthetic process	35	1	0.82	5	0.00020	0.0002

	GO:0000184	GO:0000469	GO:0000724	GO:0000725	GO:0000731	GO:0006090	GO:0006163	GO:0006165	GO:0006275	GO:0006301	⋯	GO:0043144	GO:0043628	GO:0044786	GO:0045003	GO:0046939	GO:0051293	GO:0051345	GO:0051647	GO:0051653	GO:0071824
GO:0006081	0.252	0.269	0.463	0.483	0.372	0.627	0.445	0.451	0.206	0.503	⋯	0.300	0.300	0.445	0.465	0.480	0.215	0.137	0.092	0.325	0.197
GO:0006082	0.243	0.261	0.439	0.460	0.356	0.776	0.483	0.490	0.200	0.479	⋯	0.288	0.288	0.424	0.440	0.521	0.208	0.131	0.087	0.311	0.186
GO:0006732	0.196	0.213	0.218	0.229	0.170	0.320	0.218	0.210	0.155	0.240	⋯	0.242	0.242	0.208	0.220	0.230	0.100	0.150	0.113	0.159	0.238
GO:0006766	0.087	0.095	0.229	0.242	0.174	0.428	0.273	0.287	0.072	0.254	⋯	0.108	0.108	0.232	0.230	0.306	0.100	0.150	0.113	0.159	0.106
GO:0006767	0.074	0.082	0.201	0.215	0.152	0.361	0.236	0.247	0.063	0.226	⋯	0.092	0.092	0.207	0.199	0.263	0.088	0.131	0.099	0.140	0.092
GO:0006790	0.236	0.250	0.254	0.263	0.198	0.384	0.252	0.248	0.181	0.277	⋯	0.289	0.289	0.241	0.260	0.270	0.115	0.174	0.133	0.183	0.278
GO:0006887	0.066	0.072	0.176	0.188	0.141	0.213	0.161	0.164	0.056	0.195	⋯	0.078	0.078	0.169	0.172	0.172	0.407	0.047	0.227	0.431	0.145
GO:0006888	0.022	0.026	0.065	0.071	0.051	0.076	0.058	0.059	0.021	0.074	⋯	0.028	0.028	0.068	0.062	0.062	0.292	0.039	0.215	0.274	0.056
GO:0007568	0.047	0.049	0.118	0.123	0.090	0.171	0.107	0.112	0.037	0.129	⋯	0.057	0.057	0.118	0.120	0.120	0.115	0.077	0.133	0.183	0.123
GO:0009064	0.218	0.242	0.342	0.371	0.288	0.583	0.435	0.368	0.192	0.386	⋯	0.258	0.258	0.333	0.330	0.391	0.129	0.100	0.067	0.200	0.126
GO:0009108	0.147	0.165	0.170	0.181	0.226	0.227	0.172	0.162	0.205	0.189	⋯	0.180	0.180	0.274	0.167	0.176	0.079	0.112	0.078	0.120	0.167
GO:0009110	0.153	0.168	0.326	0.346	0.355	0.460	0.351	0.355	0.213	0.358	⋯	0.181	0.181	0.486	0.321	0.375	0.187	0.106	0.071	0.269	0.154
GO:0022413	0.056	0.058	0.061	0.063	0.046	0.090	0.058	0.058	0.043	0.066	⋯	0.068	0.068	0.060	0.062	0.062	0.061	0.089	0.153	0.093	0.142
GO:0032505	0.060	0.062	0.065	0.067	0.049	0.102	0.062	0.063	0.046	0.071	⋯	0.074	0.074	0.064	0.068	0.067	0.066	0.099	0.181	0.103	0.166
GO:0032940	0.078	0.085	0.204	0.215	0.163	0.253	0.187	0.192	0.065	0.223	⋯	0.093	0.093	0.195	0.202	0.202	0.464	0.054	0.259	0.490	0.168
GO:0042364	0.132	0.147	0.289	0.310	0.314	0.400	0.310	0.311	0.186	0.321	⋯	0.157	0.157	0.435	0.281	0.329	0.166	0.095	0.064	0.241	0.138
GO:0043094	0.188	0.205	0.210	0.221	0.275	0.300	0.210	0.202	0.250	0.231	⋯	0.231	0.231	0.335	0.211	0.220	0.096	0.142	0.104	0.150	0.220
GO:0044272	0.179	0.195	0.200	0.211	0.265	0.279	0.201	0.193	0.242	0.221	⋯	0.218	0.218	0.321	0.200	0.209	0.092	0.133	0.094	0.141	0.201
GO:0044281	0.105	0.111	0.266	0.277	0.201	0.516	0.320	0.339	0.084	0.291	⋯	0.128	0.128	0.266	0.270	0.361	0.115	0.174	0.133	0.183	0.123
GO:0044283	0.080	0.087	0.211	0.223	0.210	0.373	0.251	0.263	0.111	0.234	⋯	0.097	0.097	0.364	0.210	0.279	0.092	0.133	0.094	0.141	0.089
GO:0044702	0.055	0.057	0.135	0.139	0.103	0.198	0.123	0.130	0.043	0.146	⋯	0.066	0.066	0.133	0.139	0.138	0.131	0.088	0.148	0.206	0.138
GO:0044710	0.128	0.132	0.313	0.322	0.237	0.462	0.280	0.296	0.099	0.339	⋯	0.155	0.155	0.309	0.323	0.316	0.134	0.206	0.159	0.215	0.148
GO:0044711	0.099	0.106	0.253	0.265	0.250	0.348	0.225	0.235	0.133	0.277	⋯	0.121	0.121	0.430	0.256	0.250	0.110	0.162	0.119	0.171	0.111
GO:0046903	0.036	0.039	0.095	0.101	0.073	0.127	0.086	0.089	0.030	0.105	⋯	0.044	0.044	0.097	0.095	0.095	0.273	0.060	0.220	0.325	0.092
GO:0046907	0.037	0.040	0.043	0.046	0.033	0.059	0.041	0.041	0.031	0.048	⋯	0.045	0.045	0.044	0.043	0.043	0.312	0.062	0.370	0.239	0.096
GO:0048193	0.027	0.030	0.074	0.080	0.058	0.090	0.067	0.068	0.024	0.083	⋯	0.032	0.032	0.077	0.072	0.072	0.321	0.045	0.240	0.307	0.065
GO:0051186	0.236	0.250	0.254	0.263	0.198	0.384	0.252	0.248	0.181	0.277	⋯	0.289	0.289	0.241	0.260	0.270	0.115	0.174	0.133	0.183	0.278
GO:0051188	0.179	0.195	0.200	0.211	0.265	0.279	0.201	0.193	0.242	0.221	⋯	0.218	0.218	0.321	0.200	0.209	0.092	0.133	0.094	0.141	0.201
GO:0051321	0.080	0.087	0.212	0.224	0.166	0.277	0.193	0.200	0.065	0.234	⋯	0.096	0.096	0.272	0.211	0.211	0.264	0.061	0.094	0.406	0.192
GO:0055086	0.458	0.482	0.609	0.639	0.546	0.478	0.782	0.741	0.395	0.661	⋯	0.514	0.514	0.585	0.604	0.777	0.176	0.098	0.064	0.248	0.139
GO:0072524	0.421	0.440	0.425	0.441	0.372	0.304	0.566	0.445	0.347	0.459	⋯	0.485	0.485	0.402	0.430	0.472	0.082	0.113	0.075	0.120	0.161
GO:0072525	0.289	0.311	0.300	0.317	0.518	0.198	0.414	0.313	0.356	0.328	⋯	0.327	0.327	0.410	0.296	0.330	0.061	0.078	0.048	0.084	0.104
GO:0072527	0.421	0.440	0.425	0.441	0.372	0.304	0.566	0.445	0.347	0.459	⋯	0.485	0.485	0.402	0.430	0.472	0.082	0.113	0.075	0.120	0.161
GO:0072528	0.289	0.311	0.300	0.317	0.518	0.198	0.414	0.313	0.356	0.328	⋯	0.327	0.327	0.410	0.296	0.330	0.061	0.078	0.048	0.084	0.104
GO:1901564	0.240	0.248	0.245	0.251	0.198	0.284	0.361	0.256	0.190	0.263	⋯	0.287	0.287	0.234	0.254	0.273	0.053	0.171	0.130	0.080	0.121
GO:1901566	0.182	0.193	0.191	0.199	0.259	0.208	0.289	0.200	0.245	0.208	⋯	0.216	0.216	0.309	0.194	0.211	0.043	0.132	0.093	0.062	0.088
GO:1901615	0.182	0.191	0.192	0.198	0.149	0.310	0.197	0.199	0.142	0.208	⋯	0.222	0.222	0.185	0.198	0.212	0.056	0.184	0.146	0.086	0.135
GO:1901617	0.136	0.147	0.149	0.156	0.222	0.220	0.155	0.153	0.208	0.163	⋯	0.164	0.164	0.274	0.150	0.163	0.045	0.138	0.100	0.065	0.094
GO:1903046	0.066	0.074	0.195	0.208	0.153	0.248	0.177	0.183	0.056	0.216	⋯	0.080	0.080	0.316	0.193	0.193	0.301	0.045	0.069	0.463	0.162