This report has goseq results for 30 minute glucose when:

  1. Genes with FDR < 0.1 marked as DE
  2. Genes from above list with positive effect marked as differentially expressed
  3. Genes from above list with negative effect marked as differentially expressed

This report was generated on June 18 2015

Goseq results also saved in csv files located on snowwhite in directory: /net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/jun3/12junReps/csv

Step 1: Load in all the necessary data/libraries

library(goseq)

## Loading required package: BiasedUrn
## Loading required package: geneLenDataBase
## Loading required package: DBI

library(qvalue)

fName <- "/net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/traits/peer_k00_GL30_all_genes.txt"
outFile <- "GL30"

data <- read.table(fName, as.is=T, header=T)

gene_length_file <- "/net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/jun3/length.composite.gene.models.gencode.v19"
gene_lengths = read.table(gene_length_file, header=T, as.is=T);
gene_lengths$gene = sapply(gene_lengths$gene, function(x){ unlist(strsplit(x, split="[.]"))[1] });

data$gene <- sapply(data$gene, function(x){ unlist(strsplit(x, split="[.]"))[1] });

data <- merge(data, gene_lengths, by="gene", all.x=T)
data <- data[order(data$p.value),]
data$q.value <- qvalue(data$p.value)$qvalues
data$rank <- seq(1,length(data[,1]))

minRow <- 20

Step 2: Create genes vectors

The first vector simply marks the top 1000 genes as differentially expressed. The second and third vectors mark the genes with positive or negative effect in the top 1000 as differentially expressed.

genes <- as.numeric(data$q.value <= 0.1)
genesPos <- as.numeric(data$q.value <= 0.1 & data$effect > 0)
genesNeg <- as.numeric(data$q.value <= 0.1 & data$effect < 0)

names(genes) <- data$gene
names(genesPos) <- data$gene
names(genesNeg) <- data$gene

There are 244 DE genes with postive effect and 686 DE genes with negative effect.

Step 3: PWFs

pwf <- nullp(genes,"hg19","ensGene",bias.data=data$length, plot.fit=FALSE)

pwfPos=nullp(genesPos,"hg19","ensGene",bias.data=data$length, plot.fit=FALSE)

pwfNeg=nullp(genesNeg,"hg19","ensGene",bias.data=data$length, plot.fit=FALSE)

Step 4: run goseq

go <- goseq(pwf,"hg19","ensGene",test.cats=c("GO:BP"))
goPos <- goseq(pwfPos,"hg19","ensGene",test.cats=c("GO:BP"))
goNeg <- goseq(pwfNeg,"hg19","ensGene",test.cats=c("GO:BP"))

rownames(go) <- NULL
rownames(goPos) <- NULL
rownames(goNeg) <- NULL

# Fix problem with some p-values being slightly more than 1
go$over_represented_pvalue[go$over_represented_pvalue>1]=1;
go$under_represented_pvalue[go$under_represented_pvalue>1]=1;
goPos$over_represented_pvalue[goPos$over_represented_pvalue>1]=1;
goPos$under_represented_pvalue[goPos$under_represented_pvalue>1]=1;
goNeg$over_represented_pvalue[goNeg$over_represented_pvalue>1]=1;
goNeg$under_represented_pvalue[goNeg$under_represented_pvalue>1]=1;

go$q.value <- qvalue(go$over_represented_pvalue)$qvalues
goPos$q.value=qvalue(goPos$over_represented_pvalue)$qvalues
goNeg$q.value=qvalue(goNeg$over_represented_pvalue)$qvalues

go$q.value2 <- qvalue(go$under_represented_pvalue)$qvalues
goPos$q.value2=qvalue(goPos$under_represented_pvalue)$qvalues
goNeg$q.value2=qvalue(goNeg$under_represented_pvalue)$qvalues

Top 1000 Results

Over enriched categories (81)

rowN <- max(minRow, sum(go$q.value<=0.05))
cat(kable(go[1:rowN,c("category","term","numInCat","numDEInCat","q.value")],format="html"));
category term numInCat numDEInCat q.value
GO:0045333 cellular respiration 158 42 0.0000000
GO:0022904 respiratory electron transport chain 105 33 0.0000000
GO:0022900 electron transport chain 106 33 0.0000000
GO:0015980 energy derivation by oxidation of organic compounds 319 56 0.0000000
GO:0006091 generation of precursor metabolites and energy 394 63 0.0000000
GO:0055114 oxidation-reduction process 896 98 0.0000000
GO:1902600 hydrogen ion transmembrane transport 84 24 0.0000000
GO:0006119 oxidative phosphorylation 70 20 0.0000001
GO:0044281 small molecule metabolic process 2955 224 0.0000003
GO:0042773 ATP synthesis coupled electron transport 54 17 0.0000003
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 17 0.0000003
GO:0015992 proton transport 112 24 0.0000009
GO:0006818 hydrogen transport 114 24 0.0000012
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 10 0.0000032
GO:0015986 ATP synthesis coupled proton transport 19 10 0.0000032
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 14 0.0000032
GO:0006164 purine nucleotide biosynthetic process 191 30 0.0000307
GO:0009145 purine nucleoside triphosphate biosynthetic process 47 14 0.0000308
GO:0009152 purine ribonucleotide biosynthetic process 185 29 0.0000475
GO:0009260 ribonucleotide biosynthetic process 198 30 0.0000620
GO:0046390 ribose phosphate biosynthetic process 201 30 0.0000829
GO:0072522 purine-containing compound biosynthetic process 204 30 0.0001057
GO:0009201 ribonucleoside triphosphate biosynthetic process 52 14 0.0001057
GO:0009206 purine ribonucleoside triphosphate biosynthetic process 46 13 0.0001383
GO:0009142 nucleoside triphosphate biosynthetic process 63 15 0.0002258
GO:0006754 ATP biosynthetic process 36 11 0.0004184
GO:0044711 single-organism biosynthetic process 1254 103 0.0006403
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 7 0.0008492
GO:0015672 monovalent inorganic cation transport 350 40 0.0008928
GO:1901566 organonitrogen compound biosynthetic process 586 57 0.0015313
GO:0009165 nucleotide biosynthetic process 259 32 0.0017872
GO:1901293 nucleoside phosphate biosynthetic process 260 32 0.0018281
GO:0044710 single-organism metabolic process 4810 308 0.0018281
GO:0042451 purine nucleoside biosynthetic process 88 16 0.0030352
GO:0046129 purine ribonucleoside biosynthetic process 88 16 0.0030352
GO:0009127 purine nucleoside monophosphate biosynthetic process 61 13 0.0030352
GO:0009168 purine ribonucleoside monophosphate biosynthetic process 61 13 0.0030352
GO:0009161 ribonucleoside monophosphate metabolic process 478 48 0.0032635
GO:0009167 purine ribonucleoside monophosphate metabolic process 466 47 0.0034755
GO:0009126 purine nucleoside monophosphate metabolic process 467 47 0.0035263
GO:0046034 ATP metabolic process 442 45 0.0039797
GO:0009156 ribonucleoside monophosphate biosynthetic process 73 14 0.0048099
GO:0042455 ribonucleoside biosynthetic process 102 17 0.0048769
GO:0009123 nucleoside monophosphate metabolic process 489 48 0.0048888
GO:0019637 organophosphate metabolic process 1770 130 0.0081385
GO:0006811 ion transport 1120 89 0.0082029
GO:0001525 angiogenesis 350 37 0.0089190
GO:0006163 purine nucleotide metabolic process 1313 101 0.0111580
GO:0098662 inorganic cation transmembrane transport 397 40 0.0116223
GO:0009124 nucleoside monophosphate biosynthetic process 80 14 0.0116702
GO:0009163 nucleoside biosynthetic process 111 17 0.0123561
GO:1901659 glycosyl compound biosynthetic process 112 17 0.0136811
GO:0009259 ribonucleotide metabolic process 1307 100 0.0139905
GO:0009150 purine ribonucleotide metabolic process 1292 99 0.0141599
GO:0034375 high-density lipoprotein particle remodeling 10 5 0.0145076
GO:0019693 ribose phosphate metabolic process 1311 100 0.0149466
GO:1901564 organonitrogen compound metabolic process 2217 154 0.0185960
GO:0055085 transmembrane transport 992 79 0.0213755
GO:0098655 cation transmembrane transport 467 44 0.0215904
GO:0034220 ion transmembrane transport 658 57 0.0225252
GO:0072521 purine-containing compound metabolic process 1346 101 0.0232516
GO:0006793 phosphorus metabolic process 3268 214 0.0240939
GO:0043691 reverse cholesterol transport 11 5 0.0261299
GO:0009117 nucleotide metabolic process 1456 107 0.0309137
GO:0043535 regulation of blood vessel endothelial cell migration 40 9 0.0310422
GO:0090407 organophosphate biosynthetic process 491 45 0.0326703
GO:0045765 regulation of angiogenesis 158 20 0.0327636
GO:0006753 nucleoside phosphate metabolic process 1461 107 0.0330744
GO:0048514 blood vessel morphogenesis 421 40 0.0332038
GO:0043534 blood vessel endothelial cell migration 59 11 0.0336562
GO:0045766 positive regulation of angiogenesis 91 14 0.0373981
GO:0098660 inorganic ion transmembrane transport 457 42 0.0428229
GO:0015988 energy coupled proton transmembrane transport, against electrochemical gradient 26 7 0.0451695
GO:0015991 ATP hydrolysis coupled proton transport 26 7 0.0451695
GO:0009144 purine nucleoside triphosphate metabolic process 1132 86 0.0460116
GO:0006796 phosphate-containing compound metabolic process 3226 209 0.0462505
GO:0010631 epithelial cell migration 161 20 0.0462505
GO:0090132 epithelium migration 161 20 0.0462505
GO:0009141 nucleoside triphosphate metabolic process 1150 87 0.0462505
GO:0043542 endothelial cell migration 115 16 0.0471485
GO:0006641 triglyceride metabolic process 93 14 0.0486150

Under enriched (1)

go <- go[order(go$under_represented_pvalue),]
rowN <- max(minRow, sum(go$q.value2<=0.05))
cat(kable(go[1:rowN,c("category","term","numInCat","numDEInCat","q.value2")],format="html"));
category term numInCat numDEInCat q.value2
5342 GO:0090304 nucleic acid metabolic process 4166 163 0.0303152
5341 GO:0016070 RNA metabolic process 3693 145 0.0908138
5340 GO:0043170 macromolecule metabolic process 7144 320 0.1833788
5339 GO:0044260 cellular macromolecule metabolic process 6484 289 0.3182213
5336 GO:0034645 cellular macromolecule biosynthetic process 3920 165 0.9240040
5335 GO:0009059 macromolecule biosynthetic process 4025 171 1.0000000
5333 GO:0006351 transcription, DNA-templated 2952 120 1.0000000
5337 GO:0006397 mRNA processing 404 8 1.0000000
5329 GO:0032774 RNA biosynthetic process 3063 126 1.0000000
5328 GO:2001141 regulation of RNA biosynthetic process 2888 118 1.0000000
5331 GO:0050776 regulation of immune response 666 18 1.0000000
5338 GO:0045088 regulation of innate immune response 243 3 1.0000000
5326 GO:0006355 regulation of transcription, DNA-templated 2851 117 1.0000000
5325 GO:0051252 regulation of RNA metabolic process 2966 123 1.0000000
5330 GO:0002252 immune effector process 504 12 1.0000000
5327 GO:0006396 RNA processing 676 19 1.0000000
5324 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 132 1.0000000
5323 GO:0010556 regulation of macromolecule biosynthetic process 3214 136 1.0000000
5322 GO:0010467 gene expression 4322 190 1.0000000
5334 GO:0002697 regulation of immune effector process 231 3 1.0000000

Positive Effect

Over enriched categories (0)

rowN <- max(minRow, sum(goPos$q.value<=0.05))
cat(kable(goPos[1:rowN,c("category","term","numInCat","numDEInCat","q.value")],format="html"));
category term numInCat numDEInCat q.value
GO:0051005 negative regulation of lipoprotein lipase activity 3 2 1
GO:0032025 response to cobalt ion 5 2 1
GO:0048102 autophagic cell death 6 2 1
GO:0070601 centromeric sister chromatid cohesion 5 2 1
GO:0006108 malate metabolic process 7 2 1
GO:0070830 tight junction assembly 39 4 1
GO:2000480 negative regulation of cAMP-dependent protein kinase activity 6 2 1
GO:2000780 negative regulation of double-strand break repair 6 2 1
GO:0006333 chromatin assembly or disassembly 110 6 1
GO:0044260 cellular macromolecule metabolic process 6484 112 1
GO:0045738 negative regulation of DNA repair 7 2 1
GO:0043297 apical junction assembly 46 4 1
GO:0031497 chromatin assembly 87 5 1
GO:0042787 protein ubiquitination involved in ubiquitin-dependent protein catabolic process 73 5 1
GO:0060192 negative regulation of lipase activity 9 2 1
GO:0044267 cellular protein metabolic process 3491 66 1
GO:0016567 protein ubiquitination 612 17 1
GO:2000479 regulation of cAMP-dependent protein kinase activity 10 2 1
GO:0034728 nucleosome organization 95 5 1
GO:0071279 cellular response to cobalt ion 1 1 1

Under enriched (0)

goPos <- goPos[order(goPos$under_represented_pvalue),]
rowN <- max(minRow, sum(goPos$q.value2<=0.05))
cat(kable(goPos[1:rowN,c("category","term","numInCat","numDEInCat","q.value2")],format="html"));
category term numInCat numDEInCat q.value2
2589 GO:1901135 carbohydrate derivative metabolic process 1917 12 1
2588 GO:1901564 organonitrogen compound metabolic process 2217 17 1
2587 GO:0006082 organic acid metabolic process 944 4 1
2586 GO:0043436 oxoacid metabolic process 934 4 1
3758 GO:0006520 cellular amino acid metabolic process 416 0 1
2585 GO:0044281 small molecule metabolic process 2955 27 1
2584 GO:0044710 single-organism metabolic process 4810 51 1
2578 GO:0019637 organophosphate metabolic process 1770 15 1
2583 GO:0019752 carboxylic acid metabolic process 829 4 1
2565 GO:0044763 single-organism cellular process 9511 120 1
2577 GO:0019693 ribose phosphate metabolic process 1311 10 1
2575 GO:0009259 ribonucleotide metabolic process 1307 10 1
2574 GO:1901565 organonitrogen compound catabolic process 1294 10 1
2570 GO:0009150 purine ribonucleotide metabolic process 1292 10 1
2576 GO:0022610 biological adhesion 916 6 1
2582 GO:0006140 regulation of nucleotide metabolic process 613 3 1
2581 GO:1900542 regulation of purine nucleotide metabolic process 610 3 1
2573 GO:0007155 cell adhesion 912 6 1
2580 GO:0002520 immune system development 648 3 1
2567 GO:1901136 carbohydrate derivative catabolic process 1164 9 1

Negative Effect

Over enriched categories (133)

category term numInCat numDEInCat q.value
GO:0045333 cellular respiration 158 41 0.0000000
GO:0022904 respiratory electron transport chain 105 33 0.0000000
GO:0022900 electron transport chain 106 33 0.0000000
GO:0006091 generation of precursor metabolites and energy 394 60 0.0000000
GO:0015980 energy derivation by oxidation of organic compounds 319 53 0.0000000
GO:0044281 small molecule metabolic process 2955 197 0.0000000
GO:0055114 oxidation-reduction process 896 87 0.0000000
GO:1902600 hydrogen ion transmembrane transport 84 23 0.0000000
GO:0006119 oxidative phosphorylation 70 20 0.0000000
GO:0042773 ATP synthesis coupled electron transport 54 17 0.0000000
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 17 0.0000000
GO:0044710 single-organism metabolic process 4810 257 0.0000000
GO:0015992 proton transport 112 23 0.0000000
GO:0006818 hydrogen transport 114 23 0.0000000
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 14 0.0000001
GO:0006164 purine nucleotide biosynthetic process 191 29 0.0000001
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 10 0.0000002
GO:0015986 ATP synthesis coupled proton transport 19 10 0.0000002
GO:0044711 single-organism biosynthetic process 1254 92 0.0000002
GO:0009152 purine ribonucleotide biosynthetic process 185 28 0.0000002
GO:0009260 ribonucleotide biosynthetic process 198 29 0.0000002
GO:0046390 ribose phosphate biosynthetic process 201 29 0.0000002
GO:0072522 purine-containing compound biosynthetic process 204 29 0.0000003
GO:1901564 organonitrogen compound metabolic process 2217 137 0.0000005
GO:0019637 organophosphate metabolic process 1770 115 0.0000009
GO:0009161 ribonucleoside monophosphate metabolic process 478 46 0.0000020
GO:0009167 purine ribonucleoside monophosphate metabolic process 466 45 0.0000026
GO:0009126 purine nucleoside monophosphate metabolic process 467 45 0.0000026
GO:1901566 organonitrogen compound biosynthetic process 586 52 0.0000027
GO:0009123 nucleoside monophosphate metabolic process 489 46 0.0000034
GO:0009259 ribonucleotide metabolic process 1307 90 0.0000036
GO:0009145 purine nucleoside triphosphate biosynthetic process 47 13 0.0000036
GO:0046034 ATP metabolic process 442 43 0.0000036
GO:0019693 ribose phosphate metabolic process 1311 90 0.0000038
GO:0009150 purine ribonucleotide metabolic process 1292 89 0.0000038
GO:0006163 purine nucleotide metabolic process 1313 90 0.0000038
GO:0072521 purine-containing compound metabolic process 1346 90 0.0000116
GO:0009201 ribonucleoside triphosphate biosynthetic process 52 13 0.0000126
GO:0006754 ATP biosynthetic process 36 11 0.0000128
GO:0009165 nucleotide biosynthetic process 259 30 0.0000148
GO:1901293 nucleoside phosphate biosynthetic process 260 30 0.0000160
GO:0009142 nucleoside triphosphate biosynthetic process 63 14 0.0000183
GO:0009206 purine ribonucleoside triphosphate biosynthetic process 46 12 0.0000212
GO:0009117 nucleotide metabolic process 1456 94 0.0000237
GO:0006753 nucleoside phosphate metabolic process 1461 94 0.0000270
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 7 0.0000655
GO:0009127 purine nucleoside monophosphate biosynthetic process 61 13 0.0000748
GO:0009168 purine ribonucleoside monophosphate biosynthetic process 61 13 0.0000748
GO:0009141 nucleoside triphosphate metabolic process 1150 77 0.0000913
GO:0055086 nucleobase-containing small molecule metabolic process 1507 94 0.0000936
GO:0009144 purine nucleoside triphosphate metabolic process 1132 76 0.0000944
GO:0009156 ribonucleoside monophosphate biosynthetic process 73 14 0.0001029
GO:0090407 organophosphate biosynthetic process 491 42 0.0001805
GO:0042451 purine nucleoside biosynthetic process 88 15 0.0001947
GO:0046129 purine ribonucleoside biosynthetic process 88 15 0.0001947
GO:0042455 ribonucleoside biosynthetic process 102 16 0.0002787
GO:0009124 nucleoside monophosphate biosynthetic process 80 14 0.0002976
GO:0009199 ribonucleoside triphosphate metabolic process 1132 74 0.0005489
GO:0006811 ion transport 1120 73 0.0005489
GO:0015672 monovalent inorganic cation transport 350 32 0.0007510
GO:0009163 nucleoside biosynthetic process 111 16 0.0007899
GO:1901135 carbohydrate derivative metabolic process 1917 110 0.0008525
GO:1901659 glycosyl compound biosynthetic process 112 16 0.0008525
GO:0009205 purine ribonucleoside triphosphate metabolic process 1126 73 0.0008525
GO:0032787 monocarboxylic acid metabolic process 427 36 0.0013709
GO:0006793 phosphorus metabolic process 3268 168 0.0013853
GO:0046128 purine ribonucleoside metabolic process 1195 75 0.0019214
GO:0009119 ribonucleoside metabolic process 1218 76 0.0019580
GO:0043534 blood vessel endothelial cell migration 59 11 0.0019580
GO:0042278 purine nucleoside metabolic process 1198 75 0.0020053
GO:0010631 epithelial cell migration 161 19 0.0021088
GO:0090132 epithelium migration 161 19 0.0021088
GO:0043535 regulation of blood vessel endothelial cell migration 40 9 0.0023881
GO:0034375 high-density lipoprotein particle remodeling 10 5 0.0024279
GO:0044283 small molecule biosynthetic process 388 33 0.0024279
GO:0090130 tissue migration 164 19 0.0026010
GO:0052652 cyclic purine nucleotide metabolic process 98 14 0.0028108
GO:0009116 nucleoside metabolic process 1238 76 0.0030678
GO:0009190 cyclic nucleotide biosynthetic process 99 14 0.0030934
GO:0098662 inorganic cation transmembrane transport 397 33 0.0031215
GO:0019752 carboxylic acid metabolic process 829 56 0.0031323
GO:0007005 mitochondrion organization 298 27 0.0035336
GO:0001525 angiogenesis 350 30 0.0042013
GO:1901657 glycosyl compound metabolic process 1252 76 0.0042126
GO:0043691 reverse cholesterol transport 11 5 0.0042516
GO:0043542 endothelial cell migration 115 15 0.0042516
GO:0006796 phosphate-containing compound metabolic process 3226 163 0.0045568
GO:0055085 transmembrane transport 992 63 0.0053743
GO:0006629 lipid metabolic process 1015 64 0.0062063
GO:0001667 ameboidal cell migration 223 22 0.0063219
GO:0010632 regulation of epithelial cell migration 119 15 0.0064634
GO:0055081 anion homeostasis 27 7 0.0068212
GO:0048514 blood vessel morphogenesis 421 33 0.0093185
GO:0010594 regulation of endothelial cell migration 84 12 0.0102025
GO:0001568 blood vessel development 480 36 0.0108166
GO:0043436 oxoacid metabolic process 934 59 0.0111043
GO:0045765 regulation of angiogenesis 158 17 0.0121616
GO:0048878 chemical homeostasis 682 46 0.0123337
GO:0098655 cation transmembrane transport 467 35 0.0126385
GO:0006082 organic acid metabolic process 944 59 0.0143420
GO:0032368 regulation of lipid transport 63 10 0.0148194
GO:0001944 vasculature development 509 37 0.0152584
GO:0045834 positive regulation of lipid metabolic process 90 12 0.0172275
GO:0098660 inorganic ion transmembrane transport 457 34 0.0172275
GO:0009187 cyclic nucleotide metabolic process 133 15 0.0174275
GO:0045766 positive regulation of angiogenesis 91 12 0.0174275
GO:0044282 small molecule catabolic process 242 22 0.0178946
GO:0032371 regulation of sterol transport 23 6 0.0192215
GO:0032374 regulation of cholesterol transport 23 6 0.0192215
GO:0046889 positive regulation of lipid biosynthetic process 43 8 0.0206201
GO:0034220 ion transmembrane transport 658 44 0.0214530
GO:0006631 fatty acid metabolic process 281 24 0.0216863
GO:0006171 cAMP biosynthetic process 80 11 0.0216999
GO:0006641 triglyceride metabolic process 93 12 0.0222765
GO:0006812 cation transport 767 49 0.0247663
GO:1901342 regulation of vasculature development 172 17 0.0293895
GO:0010596 negative regulation of endothelial cell migration 25 6 0.0294452
GO:0009060 aerobic respiration 46 8 0.0311339
GO:0034367 macromolecular complex remodeling 17 5 0.0311346
GO:0034368 protein-lipid complex remodeling 17 5 0.0311346
GO:0034369 plasma lipoprotein particle remodeling 17 5 0.0311346
GO:0044255 cellular lipid metabolic process 772 49 0.0326427
GO:0043537 negative regulation of blood vessel endothelial cell migration 17 5 0.0331828
GO:0006639 acylglycerol metabolic process 98 12 0.0334215
GO:0015988 energy coupled proton transmembrane transport, against electrochemical gradient 26 6 0.0339360
GO:0015991 ATP hydrolysis coupled proton transport 26 6 0.0339360
GO:0010633 negative regulation of epithelial cell migration 36 7 0.0348287
GO:0006638 neutral lipid metabolic process 99 12 0.0356737
GO:0019216 regulation of lipid metabolic process 210 19 0.0420706
GO:0042592 homeostatic process 1088 63 0.0430485
GO:0030334 regulation of cell migration 468 33 0.0454642
GO:0034384 high-density lipoprotein particle clearance 5 3 0.0468349
GO:0007007 inner mitochondrial membrane organization 11 4 0.0475367

Under enriched (17)

category term numInCat numDEInCat q.value2
4840 GO:0090304 nucleic acid metabolic process 4166 96 0.0000018
4839 GO:0043170 macromolecule metabolic process 7144 201 0.0000018
4838 GO:0044260 cellular macromolecule metabolic process 6484 177 0.0000018
4837 GO:0016070 RNA metabolic process 3693 88 0.0000947
4836 GO:0010556 regulation of macromolecule biosynthetic process 3214 79 0.0034772
4835 GO:0006351 transcription, DNA-templated 2952 71 0.0036938
4834 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 77 0.0036938
4833 GO:0010467 gene expression 4322 117 0.0037426
4832 GO:2001141 regulation of RNA biosynthetic process 2888 70 0.0037426
4831 GO:0034645 cellular macromolecule biosynthetic process 3920 104 0.0037426
4829 GO:0010468 regulation of gene expression 3465 89 0.0037426
4830 GO:0006355 regulation of transcription, DNA-templated 2851 69 0.0037426
4826 GO:0009059 macromolecule biosynthetic process 4025 108 0.0037928
4827 GO:0051252 regulation of RNA metabolic process 2966 73 0.0037928
4825 GO:0032774 RNA biosynthetic process 3063 77 0.0060402
4824 GO:0060255 regulation of macromolecule metabolic process 4402 123 0.0082459
4828 GO:0006397 mRNA processing 404 2 0.0143151
4823 GO:0031326 regulation of cellular biosynthetic process 3340 91 0.0507937
4822 GO:0009889 regulation of biosynthetic process 3367 93 0.0784768
4818 GO:0050794 regulation of cellular process 7722 253 0.1602316

Final Step: csv output

write.csv(go,file=paste("csv/", outFile,"_main.csv",sep=''), row.names=FALSE)
write.csv(goPos,file=paste("csv/", outFile,"Pos.csv",sep=''), row.names=FALSE)
write.csv(goNeg,file=paste("csv/", outFile,"Neg.csv",sep=''), row.names=FALSE)