This report has goseq results for 60 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_k01_GL60_all_genes.txt"
outFile <- "GL60"

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 839 DE genes with postive effect and 746 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 (16)

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 46 0.0000000
GO:0022904 respiratory electron transport chain 105 34 0.0000000
GO:0022900 electron transport chain 106 34 0.0000000
GO:0015980 energy derivation by oxidation of organic compounds 319 64 0.0000001
GO:0006091 generation of precursor metabolites and energy 394 73 0.0000003
GO:0055114 oxidation-reduction process 896 129 0.0000028
GO:1902600 hydrogen ion transmembrane transport 84 21 0.0032164
GO:0042773 ATP synthesis coupled electron transport 54 16 0.0032164
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 16 0.0032164
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 8 0.0042008
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 9 0.0049283
GO:0015986 ATP synthesis coupled proton transport 19 9 0.0049283
GO:0006119 oxidative phosphorylation 70 18 0.0059398
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 13 0.0094368
GO:0046390 ribose phosphate biosynthetic process 201 35 0.0367030
GO:0044281 small molecule metabolic process 2955 316 0.0373474
GO:0009260 ribonucleotide biosynthetic process 198 34 0.0554088
GO:0071478 cellular response to radiation 116 23 0.1111374
GO:0044710 single-organism metabolic process 4810 483 0.1111374
GO:0071482 cellular response to light stimulus 74 17 0.1111374

Under enriched (0)

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
6479 GO:0002831 regulation of response to biotic stimulus 97 1 1
6477 GO:0002697 regulation of immune effector process 231 8 1
6476 GO:0051090 regulation of sequence-specific DNA binding transcription factor activity 304 13 1
6471 GO:0016070 RNA metabolic process 3693 284 1
6478 GO:0060491 regulation of cell projection assembly 88 1 1
6464 GO:0043207 response to external biotic stimulus 535 30 1
6465 GO:0051707 response to other organism 535 30 1
6463 GO:0034660 ncRNA metabolic process 325 16 1
6469 GO:0006643 membrane lipid metabolic process 148 5 1
6473 GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity 116 3 1
6458 GO:0031347 regulation of defense response 462 26 1
6474 GO:0006892 post-Golgi vesicle-mediated transport 93 2 1
6472 GO:0006661 phosphatidylinositol biosynthetic process 91 2 1
9692 GO:0045839 negative regulation of mitosis 50 0 1
6447 GO:0090304 nucleic acid metabolic process 4166 331 1
9554 GO:0043038 amino acid activation 50 0 1
9555 GO:0043039 tRNA aminoacylation 50 0 1
6457 GO:0043900 regulation of multi-organism process 273 13 1
6462 GO:0070588 calcium ion transmembrane transport 140 5 1
6475 GO:0050688 regulation of defense response to virus 71 1 1

Positive Effect

Over enriched categories (85)

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:0007049 cell cycle 1450 125 0.0000006
GO:0022402 cell cycle process 1086 98 0.0000058
GO:0044260 cellular macromolecule metabolic process 6484 387 0.0000067
GO:0031325 positive regulation of cellular metabolic process 1991 143 0.0004749
GO:0043170 macromolecule metabolic process 7144 406 0.0005521
GO:0048522 positive regulation of cellular process 3307 213 0.0005521
GO:0043412 macromolecule modification 2854 192 0.0005521
GO:0051276 chromosome organization 738 67 0.0006346
GO:0048518 positive regulation of biological process 3684 231 0.0007890
GO:0009893 positive regulation of metabolic process 2104 146 0.0013473
GO:0006464 cellular protein modification process 2739 184 0.0013473
GO:0036211 protein modification process 2739 184 0.0013473
GO:0000278 mitotic cell cycle 856 73 0.0013770
GO:0032268 regulation of cellular protein metabolic process 1414 106 0.0016659
GO:0010604 positive regulation of macromolecule metabolic process 1913 134 0.0024728
GO:1903047 mitotic cell cycle process 746 65 0.0024728
GO:0032446 protein modification by small protein conjugation 654 59 0.0027173
GO:0044267 cellular protein metabolic process 3491 220 0.0027173
GO:0071478 cellular response to radiation 116 18 0.0054834
GO:0044843 cell cycle G1/S phase transition 238 28 0.0054834
GO:0006521 regulation of cellular amino acid metabolic process 59 12 0.0054834
GO:0070647 protein modification by small protein conjugation or removal 731 63 0.0054834
GO:0016567 protein ubiquitination 612 55 0.0054834
GO:0006259 DNA metabolic process 838 68 0.0054978
GO:0032270 positive regulation of cellular protein metabolic process 868 70 0.0083582
GO:0010498 proteasomal protein catabolic process 284 31 0.0090106
GO:0090068 positive regulation of cell cycle process 196 24 0.0090106
GO:0000077 DNA damage checkpoint 148 20 0.0090543
GO:0000082 G1/S transition of mitotic cell cycle 236 27 0.0096008
GO:0071214 cellular response to abiotic stimulus 208 25 0.0099189
GO:0060255 regulation of macromolecule metabolic process 4402 262 0.0109168
GO:0031571 mitotic G1 DNA damage checkpoint 75 13 0.0109168
GO:0033238 regulation of cellular amine metabolic process 76 13 0.0109168
GO:1902806 regulation of cell cycle G1/S phase transition 128 18 0.0109168
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest 66 12 0.0109168
GO:0051443 positive regulation of ubiquitin-protein transferase activity 86 14 0.0109168
GO:0000738 DNA catabolic process, exonucleolytic 21 7 0.0109168
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process 265 29 0.0109168
GO:0044819 mitotic G1/S transition checkpoint 76 13 0.0109168
GO:0044783 G1 DNA damage checkpoint 76 13 0.0109168
GO:0031323 regulation of cellular metabolic process 4749 280 0.0109168
GO:0031570 DNA integrity checkpoint 154 20 0.0109168
GO:0072431 signal transduction involved in mitotic G1 DNA damage checkpoint 67 12 0.0109168
GO:1902400 intracellular signal transduction involved in G1 DNA damage checkpoint 67 12 0.0109168
GO:0006325 chromatin organization 563 50 0.0109196
GO:0071482 cellular response to light stimulus 74 13 0.0109686
GO:0006974 cellular response to DNA damage stimulus 668 55 0.0109686
GO:0072401 signal transduction involved in DNA integrity checkpoint 68 12 0.0109686
GO:0072413 signal transduction involved in mitotic cell cycle checkpoint 68 12 0.0109686
GO:0072422 signal transduction involved in DNA damage checkpoint 68 12 0.0109686
GO:1902402 signal transduction involved in mitotic DNA damage checkpoint 68 12 0.0109686
GO:1902403 signal transduction involved in mitotic DNA integrity checkpoint 68 12 0.0109686
GO:0044770 cell cycle phase transition 455 42 0.0121661
GO:0034644 cellular response to UV 47 10 0.0121661
GO:0051351 positive regulation of ligase activity 90 14 0.0121661
GO:0072395 signal transduction involved in cell cycle checkpoint 69 12 0.0121661
GO:0010467 gene expression 4322 254 0.0135027
GO:0090304 nucleic acid metabolic process 4166 246 0.0153012
GO:2000045 regulation of G1/S transition of mitotic cell cycle 126 17 0.0182118
GO:0071103 DNA conformation change 173 21 0.0184090
GO:0010608 posttranscriptional regulation of gene expression 422 39 0.0184090
GO:0019222 regulation of metabolic process 5252 302 0.0185029
GO:0009411 response to UV 112 16 0.0185029
GO:0006323 DNA packaging 117 16 0.0190668
GO:0051247 positive regulation of protein metabolic process 953 72 0.0191548
GO:0033554 cellular response to stress 1339 94 0.0192728
GO:0071340 skeletal muscle acetylcholine-gated channel clustering 6 4 0.0192728
GO:0051347 positive regulation of transferase activity 534 46 0.0195548
GO:0000209 protein polyubiquitination 187 22 0.0201294
GO:0016568 chromatin modification 502 45 0.0201294
GO:0044237 cellular metabolic process 8652 462 0.0226913
GO:0008150 biological_process 13154 655 0.0227363
GO:0031497 chromatin assembly 87 13 0.0231655
GO:0044772 mitotic cell cycle phase transition 447 40 0.0252011
GO:0006333 chromatin assembly or disassembly 110 15 0.0257253
GO:1902807 negative regulation of cell cycle G1/S phase transition 96 14 0.0257253
GO:2000134 negative regulation of G1/S transition of mitotic cell cycle 96 14 0.0257253
GO:0051246 regulation of protein metabolic process 1748 116 0.0262804
GO:0010564 regulation of cell cycle process 437 39 0.0292302
GO:0031399 regulation of protein modification process 1110 80 0.0295117
GO:0051726 regulation of cell cycle 757 59 0.0327971
GO:0051438 regulation of ubiquitin-protein transferase activity 102 14 0.0393165
GO:0097345 mitochondrial outer membrane permeabilization 50 9 0.0469644
GO:0071158 positive regulation of cell cycle arrest 82 12 0.0472410
GO:0044238 primary metabolic process 8725 463 0.0484584

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
4867 Other NA 1443 40 1
4866 GO:0007600 sensory perception 334 4 1
4865 GO:0007009 plasma membrane organization 169 1 1
7612 GO:0043112 receptor metabolic process 120 0 1
4864 GO:0098609 cell-cell adhesion 148 1 1
4863 GO:0001667 ameboidal cell migration 223 3 1
6924 GO:0006414 translational elongation 121 0 1
4862 GO:0002697 regulation of immune effector process 231 3 1
4854 GO:0000904 cell morphogenesis involved in differentiation 701 21 1
7045 GO:0009063 cellular amino acid catabolic process 103 0 1
4847 GO:0032989 cellular component morphogenesis 1059 37 1
4848 GO:0050877 neurological system process 626 18 1
4861 GO:0060560 developmental growth involved in morphogenesis 127 1 1
4851 GO:0006790 sulfur compound metabolic process 292 6 1
4858 GO:0090130 tissue migration 164 2 1
4860 GO:0072659 protein localization to plasma membrane 129 1 1
8012 GO:0060491 regulation of cell projection assembly 88 0 1
4855 GO:0010631 epithelial cell migration 161 2 1
4856 GO:0090132 epithelium migration 161 2 1
4859 GO:0021953 central nervous system neuron differentiation 123 1 1

Negative Effect

Over enriched categories (106)

category term numInCat numDEInCat q.value
GO:0045333 cellular respiration 158 43 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 53 0.0000000
GO:0006091 generation of precursor metabolites and energy 394 58 0.0000000
GO:0055114 oxidation-reduction process 896 88 0.0000000
GO:0044281 small molecule metabolic process 2955 195 0.0000000
GO:1902600 hydrogen ion transmembrane transport 84 20 0.0000000
GO:0006119 oxidative phosphorylation 70 17 0.0000008
GO:0042773 ATP synthesis coupled electron transport 54 15 0.0000008
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 15 0.0000008
GO:0009260 ribonucleotide biosynthetic process 198 28 0.0000050
GO:0046390 ribose phosphate biosynthetic process 201 28 0.0000061
GO:0015992 proton transport 112 20 0.0000067
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 9 0.0000069
GO:0015986 ATP synthesis coupled proton transport 19 9 0.0000069
GO:0006818 hydrogen transport 114 20 0.0000077
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 8 0.0000077
GO:0006811 ion transport 1120 83 0.0000088
GO:0044711 single-organism biosynthetic process 1254 90 0.0000098
GO:0009152 purine ribonucleotide biosynthetic process 185 26 0.0000112
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 12 0.0000136
GO:1901566 organonitrogen compound biosynthetic process 586 52 0.0000190
GO:0006164 purine nucleotide biosynthetic process 191 26 0.0000193
GO:0072522 purine-containing compound biosynthetic process 204 26 0.0000719
GO:0009165 nucleotide biosynthetic process 259 30 0.0000727
GO:1901293 nucleoside phosphate biosynthetic process 260 30 0.0000763
GO:1901564 organonitrogen compound metabolic process 2217 133 0.0001305
GO:0019637 organophosphate metabolic process 1770 111 0.0001941
GO:0044710 single-organism metabolic process 4810 247 0.0002005
GO:0015672 monovalent inorganic cation transport 350 35 0.0002224
GO:0001525 angiogenesis 350 35 0.0002453
GO:0006754 ATP biosynthetic process 36 10 0.0002657
GO:0034220 ion transmembrane transport 658 53 0.0003165
GO:0048514 blood vessel morphogenesis 421 39 0.0003882
GO:0009145 purine nucleoside triphosphate biosynthetic process 47 11 0.0004695
GO:0009259 ribonucleotide metabolic process 1307 87 0.0005436
GO:0009161 ribonucleoside monophosphate metabolic process 478 42 0.0005436
GO:0009117 nucleotide metabolic process 1456 94 0.0005436
GO:0019693 ribose phosphate metabolic process 1311 87 0.0005681
GO:0006753 nucleoside phosphate metabolic process 1461 94 0.0005936
GO:0009123 nucleoside monophosphate metabolic process 489 42 0.0008553
GO:0009150 purine ribonucleotide metabolic process 1292 85 0.0009911
GO:0046034 ATP metabolic process 442 39 0.0010296
GO:0009201 ribonucleoside triphosphate biosynthetic process 52 11 0.0011422
GO:0009156 ribonucleoside monophosphate biosynthetic process 73 13 0.0012270
GO:0001568 blood vessel development 480 41 0.0012500
GO:0040012 regulation of locomotion 533 44 0.0012540
GO:0009142 nucleoside triphosphate biosynthetic process 63 12 0.0013001
GO:0009167 purine ribonucleoside monophosphate metabolic process 466 40 0.0013220
GO:0009126 purine nucleoside monophosphate metabolic process 467 40 0.0013477
GO:0030334 regulation of cell migration 468 40 0.0014000
GO:0051270 regulation of cellular component movement 555 45 0.0014738
GO:0006163 purine nucleotide metabolic process 1313 85 0.0016305
GO:0052652 cyclic purine nucleotide metabolic process 98 15 0.0016310
GO:0009190 cyclic nucleotide biosynthetic process 99 15 0.0017791
GO:0009206 purine ribonucleoside triphosphate biosynthetic process 46 10 0.0017791
GO:2000145 regulation of cell motility 492 41 0.0017791
GO:0001944 vasculature development 509 42 0.0017791
GO:0007267 cell-cell signaling 915 64 0.0017791
GO:0055085 transmembrane transport 992 68 0.0018869
GO:0055086 nucleobase-containing small molecule metabolic process 1507 94 0.0018869
GO:0006099 tricarboxylic acid cycle 28 8 0.0019853
GO:0009124 nucleoside monophosphate biosynthetic process 80 13 0.0024731
GO:0090407 organophosphate biosynthetic process 491 40 0.0032694
GO:0043436 oxoacid metabolic process 934 64 0.0032913
GO:0072521 purine-containing compound metabolic process 1346 85 0.0034124
GO:0009127 purine nucleoside monophosphate biosynthetic process 61 11 0.0037205
GO:0009168 purine ribonucleoside monophosphate biosynthetic process 61 11 0.0037205
GO:0019752 carboxylic acid metabolic process 829 58 0.0042560
GO:0006082 organic acid metabolic process 944 64 0.0042560
GO:0048870 cell motility 948 64 0.0049583
GO:0051674 localization of cell 948 64 0.0049583
GO:0040011 locomotion 1247 79 0.0053220
GO:0006812 cation transport 767 54 0.0060957
GO:0044283 small molecule biosynthetic process 388 33 0.0067921
GO:0016477 cell migration 887 60 0.0079262
GO:0032787 monocarboxylic acid metabolic process 427 35 0.0084750
GO:0015711 organic anion transport 293 27 0.0085964
GO:0044763 single-organism cellular process 9511 425 0.0087438
GO:0045765 regulation of angiogenesis 158 18 0.0087438
GO:0009060 aerobic respiration 46 9 0.0103678
GO:0009187 cyclic nucleotide metabolic process 133 16 0.0121924
GO:0048646 anatomical structure formation involved in morphogenesis 855 57 0.0193113
GO:0098662 inorganic cation transmembrane transport 397 32 0.0211552
GO:0098655 cation transmembrane transport 467 36 0.0211552
GO:2000737 negative regulation of stem cell differentiation 8 4 0.0218551
GO:0048731 system development 3248 168 0.0220686
GO:1901342 regulation of vasculature development 172 18 0.0246159
GO:0035924 cellular response to vascular endothelial growth factor stimulus 31 7 0.0257956
GO:0042455 ribonucleoside biosynthetic process 102 13 0.0260134
GO:0061448 connective tissue development 186 19 0.0260134
GO:0098660 inorganic ion transmembrane transport 457 35 0.0266965
GO:0009141 nucleoside triphosphate metabolic process 1150 71 0.0277470
GO:0032501 multicellular organismal process 4965 240 0.0277470
GO:0044707 single-multicellular organism process 4822 234 0.0277470
GO:0009144 purine nucleoside triphosphate metabolic process 1132 70 0.0288044
GO:0009199 ribonucleoside triphosphate metabolic process 1132 70 0.0288044
GO:0006793 phosphorus metabolic process 3268 168 0.0289428
GO:1901135 carbohydrate derivative metabolic process 1917 107 0.0302049
GO:0006820 anion transport 376 30 0.0355185
GO:0006171 cAMP biosynthetic process 80 11 0.0391566
GO:0009205 purine ribonucleoside triphosphate metabolic process 1126 69 0.0395175
GO:0072358 cardiovascular system development 771 51 0.0432761
GO:0072359 circulatory system development 771 51 0.0432761
GO:0006928 cellular component movement 1405 82 0.0449544

Under enriched (47)

category term numInCat numDEInCat q.value2
8572 GO:0090304 nucleic acid metabolic process 4166 85 0.0000000
8573 GO:0043170 macromolecule metabolic process 7144 197 0.0000000
8578 GO:0044260 cellular macromolecule metabolic process 6484 173 0.0000000
8584 GO:0016070 RNA metabolic process 3693 77 0.0000000
8744 GO:0010467 gene expression 4322 102 0.0000000
12674 GO:0009059 macromolecule biosynthetic process 4025 97 0.0000000
7715 GO:0034645 cellular macromolecule biosynthetic process 3920 94 0.0000001
7371 GO:0010468 regulation of gene expression 3465 79 0.0000001
7373 GO:0010556 regulation of macromolecule biosynthetic process 3214 71 0.0000001
4711 GO:0060255 regulation of macromolecule metabolic process 4402 114 0.0000014
4710 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 71 0.0000014
4709 GO:0006351 transcription, DNA-templated 2952 66 0.0000024
4708 GO:2001141 regulation of RNA biosynthetic process 2888 65 0.0000047
4707 GO:0051252 regulation of RNA metabolic process 2966 68 0.0000056
4706 GO:0032774 RNA biosynthetic process 3063 71 0.0000056
4705 GO:0006355 regulation of transcription, DNA-templated 2851 65 0.0000088
4704 GO:0031326 regulation of cellular biosynthetic process 3340 84 0.0000500
4703 GO:0031323 regulation of cellular metabolic process 4749 134 0.0000500
4702 GO:0009889 regulation of biosynthetic process 3367 86 0.0000913
4701 GO:0019222 regulation of metabolic process 5252 156 0.0002637
4699 GO:0051171 regulation of nitrogen compound metabolic process 3754 103 0.0004798
4696 GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 102 0.0012887
4700 GO:0044257 cellular protein catabolic process 485 3 0.0014345
4695 GO:0080090 regulation of primary metabolic process 4733 141 0.0015044
4697 GO:0022402 cell cycle process 1086 18 0.0015044
4698 GO:0051603 proteolysis involved in cellular protein catabolic process 470 3 0.0021259
4694 GO:0007049 cell cycle 1450 29 0.0021259
4691 GO:0006396 RNA processing 676 8 0.0043598
4690 GO:1903047 mitotic cell cycle process 746 10 0.0045111
4687 GO:0000278 mitotic cell cycle 856 13 0.0049632
4689 GO:0006974 cellular response to DNA damage stimulus 668 8 0.0049747
4693 GO:0043632 modification-dependent macromolecule catabolic process 437 3 0.0057104
4683 GO:0006139 nucleobase-containing compound metabolic process 5435 171 0.0060630
4692 GO:0019941 modification-dependent protein catabolic process 433 3 0.0062182
4688 GO:0006511 ubiquitin-dependent protein catabolic process 424 3 0.0082200
4680 GO:0046483 heterocycle metabolic process 5565 177 0.0083643
4686 GO:0030163 protein catabolic process 596 7 0.0088458
4678 GO:0006725 cellular aromatic compound metabolic process 5569 178 0.0107641
4682 GO:0016482 cytoplasmic transport 825 13 0.0107641
4675 GO:1901360 organic cyclic compound metabolic process 5728 185 0.0147314
4684 GO:0006397 mRNA processing 404 3 0.0163220
4677 GO:0006259 DNA metabolic process 838 14 0.0191482
4676 GO:0044265 cellular macromolecule catabolic process 798 13 0.0198156
4681 GO:0006281 DNA repair 393 3 0.0219609
4685 GO:0010498 proteasomal protein catabolic process 284 1 0.0292052
4669 GO:0033554 cellular response to stress 1339 30 0.0380487
4674 GO:0000280 nuclear division 460 5 0.0393901

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)