This report has goseq results for 30 minute insulin 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_k03_S_Insu_30_all_genes.txt"
outFile <- "S_Insu_30"

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 3663 DE genes with postive effect and 3597 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 (61)

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:0006414 translational elongation 121 86 0.0000000
GO:0006413 translational initiation 167 110 0.0000000
GO:0006415 translational termination 95 71 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 80 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 73 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 74 0.0000000
GO:0045047 protein targeting to ER 110 74 0.0000001
GO:0043624 cellular protein complex disassembly 174 107 0.0000001
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 74 0.0000001
GO:0006612 protein targeting to membrane 171 104 0.0000003
GO:0043241 protein complex disassembly 195 115 0.0000006
GO:0070972 protein localization to endoplasmic reticulum 128 80 0.0000029
GO:0032984 macromolecular complex disassembly 205 117 0.0000035
GO:0002757 immune response-activating signal transduction 333 176 0.0000102
GO:0006412 translation 496 242 0.0000331
GO:0045321 leukocyte activation 561 269 0.0000900
GO:0019083 viral transcription 158 90 0.0001470
GO:0044033 multi-organism metabolic process 178 99 0.0001887
GO:0019080 viral gene expression 168 94 0.0002325
GO:0002253 activation of immune response 373 187 0.0002477
GO:0090150 establishment of protein localization to membrane 296 151 0.0002876
GO:1902578 single-organism localization 426 208 0.0002876
GO:1902580 single-organism cellular localization 426 208 0.0002876
GO:0046649 lymphocyte activation 480 231 0.0003135
GO:0072657 protein localization to membrane 371 183 0.0004199
GO:0071822 protein complex subunit organization 1283 563 0.0008409
GO:0043933 macromolecular complex subunit organization 1450 630 0.0008986
GO:0002764 immune response-regulating signaling pathway 428 209 0.0009308
GO:0050778 positive regulation of immune response 441 213 0.0009414
GO:0006402 mRNA catabolic process 196 105 0.0011632
GO:0006401 RNA catabolic process 222 116 0.0012931
GO:0000956 nuclear-transcribed mRNA catabolic process 184 99 0.0014474
GO:0031294 lymphocyte costimulation 63 41 0.0023843
GO:0031295 T cell costimulation 63 41 0.0023843
GO:0050851 antigen receptor-mediated signaling pathway 138 78 0.0026875
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 108 0.0029396
GO:0042110 T cell activation 347 170 0.0029810
GO:0006968 cellular defense response 45 31 0.0041041
GO:0006417 regulation of translation 249 127 0.0067417
GO:0002684 positive regulation of immune system process 610 279 0.0067874
GO:0050776 regulation of immune response 666 303 0.0068777
GO:0006955 immune response 1137 492 0.0068777
GO:0022904 respiratory electron transport chain 105 58 0.0107377
GO:0022411 cellular component disassembly 412 195 0.0129242
GO:0006091 generation of precursor metabolites and energy 394 185 0.0138639
GO:0022900 electron transport chain 106 58 0.0148800
GO:0072594 establishment of protein localization to organelle 456 212 0.0149068
GO:0019058 viral life cycle 303 146 0.0150866
GO:0001775 cell activation 767 341 0.0150866
GO:0050867 positive regulation of cell activation 239 119 0.0151635
GO:0002696 positive regulation of leukocyte activation 230 114 0.0265410
GO:0015671 oxygen transport 11 10 0.0265410
GO:0051251 positive regulation of lymphocyte activation 212 106 0.0314993
GO:0002682 regulation of immune system process 997 431 0.0344316
GO:0061024 membrane organization 778 343 0.0344316
GO:0050870 positive regulation of T cell activation 165 85 0.0344631
GO:0045333 cellular respiration 158 80 0.0370924
GO:0002274 myeloid leukocyte activation 123 66 0.0370924
GO:0044802 single-organism membrane organization 638 285 0.0370924
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 320 0.0429670
GO:0044419 interspecies interaction between organisms 727 320 0.0429670

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
10327 GO:0002088 lens development in camera-type eye 53 9 1
11650 GO:0050651 dermatan sulfate proteoglycan biosynthetic process 14 0 1
10322 GO:0001841 neural tube formation 90 21 1
11793 GO:0060442 branching involved in prostate gland morphogenesis 13 0 1
10319 GO:0006987 activation of signaling protein activity involved in unfolded protein response 63 13 1
10324 GO:0019933 cAMP-mediated signaling 35 5 1
10326 GO:0010226 response to lithium ion 18 1 1
10310 GO:0032075 positive regulation of nuclease activity 65 14 1
10302 GO:0007224 smoothened signaling pathway 105 27 1
10297 GO:0045165 cell fate commitment 172 48 1
10307 GO:0098661 inorganic anion transmembrane transport 70 16 1
10306 GO:0032069 regulation of nuclease activity 71 16 1
10283 GO:0009166 nucleotide catabolic process 1071 371 1
11000 GO:0030252 growth hormone secretion 11 0 1
10300 GO:0014020 primary neural tube formation 79 19 1
10277 GO:0006974 cellular response to DNA damage stimulus 668 221 1
10997 GO:0030208 dermatan sulfate biosynthetic process 11 0 1
10268 GO:1901292 nucleoside phosphate catabolic process 1077 374 1
10320 GO:0051905 establishment of pigment granule localization 20 2 1
10305 GO:0019935 cyclic-nucleotide-mediated signaling 43 8 1

Positive Effect

Over enriched categories (227)

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:0006955 immune response 1137 356 0.0000000
GO:0045321 leukocyte activation 561 205 0.0000000
GO:0002376 immune system process 1936 540 0.0000000
GO:0046649 lymphocyte activation 480 176 0.0000000
GO:0001775 cell activation 767 249 0.0000000
GO:0050776 regulation of immune response 666 222 0.0000000
GO:0002682 regulation of immune system process 997 304 0.0000000
GO:0042110 T cell activation 347 135 0.0000000
GO:0002757 immune response-activating signal transduction 333 131 0.0000000
GO:0050778 positive regulation of immune response 441 157 0.0000000
GO:0002684 positive regulation of immune system process 610 201 0.0000000
GO:0002253 activation of immune response 373 136 0.0000000
GO:0050851 antigen receptor-mediated signaling pathway 138 65 0.0000000
GO:0002764 immune response-regulating signaling pathway 428 148 0.0000000
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 85 0.0000000
GO:0002694 regulation of leukocyte activation 340 122 0.0000000
GO:0022904 respiratory electron transport chain 105 50 0.0000000
GO:0022900 electron transport chain 106 50 0.0000000
GO:0051249 regulation of lymphocyte activation 298 107 0.0000000
GO:0050865 regulation of cell activation 366 125 0.0000000
GO:0006952 defense response 1178 320 0.0000000
GO:0050900 leukocyte migration 271 97 0.0000001
GO:0050863 regulation of T cell activation 226 85 0.0000001
GO:0045333 cellular respiration 158 64 0.0000002
GO:0070661 leukocyte proliferation 200 77 0.0000002
GO:0002696 positive regulation of leukocyte activation 230 85 0.0000003
GO:0045087 innate immune response 724 209 0.0000003
GO:0050867 positive regulation of cell activation 239 87 0.0000004
GO:0032943 mononuclear cell proliferation 191 74 0.0000004
GO:0031294 lymphocyte costimulation 63 34 0.0000005
GO:0031295 T cell costimulation 63 34 0.0000005
GO:0044763 single-organism cellular process 9511 2037 0.0000005
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 107 0.0000005
GO:0046651 lymphocyte proliferation 189 73 0.0000005
GO:0051251 positive regulation of lymphocyte activation 212 79 0.0000005
GO:0050896 response to stimulus 6126 1362 0.0000005
GO:0050870 positive regulation of T cell activation 165 66 0.0000005
GO:0002274 myeloid leukocyte activation 123 53 0.0000009
GO:0002252 immune effector process 504 153 0.0000010
GO:0006935 chemotaxis 558 166 0.0000012
GO:0042330 taxis 558 166 0.0000012
GO:0072676 lymphocyte migration 47 27 0.0000018
GO:0007165 signal transduction 4077 936 0.0000027
GO:0050852 T cell receptor signaling pathway 106 47 0.0000036
GO:0044699 single-organism process 10471 2211 0.0000044
GO:0050853 B cell receptor signaling pathway 39 24 0.0000055
GO:0043207 response to external biotic stimulus 535 155 0.0000127
GO:0051707 response to other organism 535 155 0.0000127
GO:0042113 B cell activation 169 64 0.0000134
GO:0006968 cellular defense response 45 25 0.0000240
GO:0007154 cell communication 4559 1026 0.0000240
GO:0023052 signaling 4496 1013 0.0000240
GO:0044700 single organism signaling 4496 1013 0.0000240
GO:0042098 T cell proliferation 135 53 0.0000278
GO:0001816 cytokine production 471 138 0.0000320
GO:0009607 response to biotic stimulus 566 160 0.0000376
GO:0060326 cell chemotaxis 177 63 0.0000511
GO:0002697 regulation of immune effector process 231 78 0.0000511
GO:0006928 cellular component movement 1405 352 0.0000560
GO:0030098 lymphocyte differentiation 235 79 0.0000741
GO:0048583 regulation of response to stimulus 2704 633 0.0001071
GO:0002443 leukocyte mediated immunity 211 71 0.0001130
GO:0098542 defense response to other organism 271 86 0.0001130
GO:0030217 T cell differentiation 167 61 0.0001183
GO:0030595 leukocyte chemotaxis 130 49 0.0001242
GO:0042773 ATP synthesis coupled electron transport 54 26 0.0001499
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 26 0.0001499
GO:0006119 oxidative phosphorylation 70 31 0.0001657
GO:0070663 regulation of leukocyte proliferation 151 55 0.0002224
GO:0002263 cell activation involved in immune response 141 52 0.0003209
GO:0002366 leukocyte activation involved in immune response 141 52 0.0003209
GO:0040011 locomotion 1247 313 0.0003602
GO:0050670 regulation of lymphocyte proliferation 146 53 0.0003602
GO:0002275 myeloid cell activation involved in immune response 54 26 0.0004013
GO:0006091 generation of precursor metabolites and energy 394 115 0.0004079
GO:0048247 lymphocyte chemotaxis 24 15 0.0004365
GO:0032944 regulation of mononuclear cell proliferation 147 53 0.0004365
GO:0009605 response to external stimulus 1589 386 0.0005138
GO:0002831 regulation of response to biotic stimulus 97 39 0.0006170
GO:0015671 oxygen transport 11 9 0.0006296
GO:0002703 regulation of leukocyte mediated immunity 109 42 0.0006623
GO:0001817 regulation of cytokine production 417 120 0.0006623
GO:0042100 B cell proliferation 57 26 0.0014054
GO:0009617 response to bacterium 298 89 0.0016687
GO:0048584 positive regulation of response to stimulus 1324 325 0.0017759
GO:0007166 cell surface receptor signaling pathway 2374 553 0.0017844
GO:0045088 regulation of innate immune response 243 77 0.0017844
GO:0002683 negative regulation of immune system process 198 65 0.0020759
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 20 0.0022464
GO:0045576 mast cell activation 40 20 0.0022792
GO:0007599 hemostasis 485 135 0.0025471
GO:0042129 regulation of T cell proliferation 108 40 0.0026113
GO:0002704 negative regulation of leukocyte mediated immunity 18 12 0.0027146
GO:0042102 positive regulation of T cell proliferation 70 29 0.0031733
GO:0050817 coagulation 483 134 0.0031733
GO:0072678 T cell migration 30 16 0.0031733
GO:0050854 regulation of antigen receptor-mediated signaling pathway 34 18 0.0031965
GO:0010818 T cell chemotaxis 14 10 0.0033676
GO:0042060 wound healing 595 160 0.0033954
GO:0022610 biological adhesion 916 234 0.0036222
GO:0007155 cell adhesion 912 233 0.0037354
GO:0016477 cell migration 887 225 0.0043451
GO:2000401 regulation of lymphocyte migration 28 15 0.0049353
GO:0035987 endodermal cell differentiation 38 19 0.0052254
GO:0007596 blood coagulation 480 132 0.0052254
GO:0006779 porphyrin-containing compound biosynthetic process 27 15 0.0055411
GO:0036336 dendritic cell migration 22 13 0.0056482
GO:0015669 gas transport 13 9 0.0058815
GO:0050864 regulation of B cell activation 82 32 0.0058974
GO:0033014 tetrapyrrole biosynthetic process 30 16 0.0059562
GO:0045055 regulated secretory pathway 55 24 0.0059562
GO:0016310 phosphorylation 1655 394 0.0059562
GO:0002521 leukocyte differentiation 353 101 0.0063628
GO:0044707 single-multicellular organism process 4822 1054 0.0066678
GO:0009620 response to fungus 23 13 0.0066942
GO:0051716 cellular response to stimulus 4976 1086 0.0066942
GO:0010819 regulation of T cell chemotaxis 8 7 0.0070008
GO:0010820 positive regulation of T cell chemotaxis 8 7 0.0070008
GO:0002218 activation of innate immune response 167 55 0.0074708
GO:0009145 purine nucleoside triphosphate biosynthetic process 47 21 0.0075850
GO:0032501 multicellular organismal process 4965 1082 0.0078359
GO:1902600 hydrogen ion transmembrane transport 84 31 0.0079243
GO:0002758 innate immune response-activating signal transduction 160 53 0.0083763
GO:0002520 immune system development 648 169 0.0089498
GO:0002440 production of molecular mediator of immune response 103 37 0.0090751
GO:0045089 positive regulation of innate immune response 196 62 0.0091886
GO:0009611 response to wounding 833 210 0.0095007
GO:1901623 regulation of lymphocyte chemotaxis 13 9 0.0102008
GO:0050663 cytokine secretion 108 38 0.0102008
GO:0070665 positive regulation of leukocyte proliferation 100 36 0.0105005
GO:0050771 negative regulation of axonogenesis 40 19 0.0105005
GO:0002407 dendritic cell chemotaxis 18 11 0.0105005
GO:0050707 regulation of cytokine secretion 90 33 0.0108847
GO:0048870 cell motility 948 235 0.0110166
GO:0051674 localization of cell 948 235 0.0110166
GO:0050777 negative regulation of immune response 60 25 0.0110166
GO:0090025 regulation of monocyte chemotaxis 13 9 0.0111364
GO:0015980 energy derivation by oxidation of organic compounds 319 90 0.0116206
GO:0070271 protein complex biogenesis 934 231 0.0119151
GO:0097529 myeloid leukocyte migration 104 36 0.0131396
GO:0050688 regulation of defense response to virus 71 28 0.0133368
GO:0006461 protein complex assembly 932 230 0.0139696
GO:0031347 regulation of defense response 462 124 0.0140829
GO:0042742 defense response to bacterium 102 35 0.0140829
GO:0015985 energy coupled proton transport, down electrochemical gradient 19 11 0.0143442
GO:0015986 ATP synthesis coupled proton transport 19 11 0.0143442
GO:0009206 purine ribonucleoside triphosphate biosynthetic process 46 20 0.0143442
GO:0051701 interaction with host 105 37 0.0144407
GO:0006954 inflammatory response 473 125 0.0145221
GO:0006783 heme biosynthetic process 21 12 0.0148314
GO:0050857 positive regulation of antigen receptor-mediated signaling pathway 13 9 0.0158943
GO:0030097 hemopoiesis 587 153 0.0160685
GO:0016337 single organismal cell-cell adhesion 283 82 0.0163360
GO:0001819 positive regulation of cytokine production 245 72 0.0166855
GO:0002507 tolerance induction 16 10 0.0175525
GO:0032609 interferon-gamma production 78 29 0.0176228
GO:0002221 pattern recognition receptor signaling pathway 158 51 0.0181315
GO:0070098 chemokine-mediated signaling pathway 37 17 0.0181315
GO:0043299 leukocyte degranulation 43 19 0.0188117
GO:0051188 cofactor biosynthetic process 132 44 0.0188117
GO:0050920 regulation of chemotaxis 108 37 0.0188117
GO:0002700 regulation of production of molecular mediator of immune response 64 25 0.0195174
GO:0002707 negative regulation of lymphocyte mediated immunity 16 10 0.0195965
GO:2000406 positive regulation of T cell migration 17 10 0.0196129
GO:0070664 negative regulation of leukocyte proliferation 50 21 0.0205498
GO:2000403 positive regulation of lymphocyte migration 20 11 0.0212955
GO:0042776 mitochondrial ATP synthesis coupled proton transport 14 9 0.0213426
GO:0045785 positive regulation of cell adhesion 149 48 0.0213426
GO:0007409 axonogenesis 469 126 0.0213426
GO:0001706 endoderm formation 46 20 0.0213426
GO:0002444 myeloid leukocyte mediated immunity 54 22 0.0213666
GO:0050671 positive regulation of lymphocyte proliferation 97 34 0.0213666
GO:0032945 negative regulation of mononuclear cell proliferation 47 20 0.0219587
GO:0050672 negative regulation of lymphocyte proliferation 47 20 0.0219587
GO:0002279 mast cell activation involved in immune response 28 14 0.0219587
GO:0002448 mast cell mediated immunity 28 14 0.0219587
GO:0034109 homotypic cell-cell adhesion 68 26 0.0223939
GO:0045058 T cell selection 34 16 0.0223939
GO:0048534 hematopoietic or lymphoid organ development 615 158 0.0225601
GO:0052548 regulation of endopeptidase activity 270 77 0.0225601
GO:0007159 leukocyte cell-cell adhesion 44 19 0.0226915
GO:0097530 granulocyte migration 71 26 0.0227329
GO:0007026 negative regulation of microtubule depolymerization 22 12 0.0232510
GO:0032946 positive regulation of mononuclear cell proliferation 98 34 0.0250601
GO:2000106 regulation of leukocyte apoptotic process 65 25 0.0252752
GO:0070228 regulation of lymphocyte apoptotic process 44 19 0.0252752
GO:0042221 response to chemical 2788 622 0.0252752
GO:0031111 negative regulation of microtubule polymerization or depolymerization 31 15 0.0254938
GO:0046631 alpha-beta T cell activation 86 31 0.0261932
GO:0006099 tricarboxylic acid cycle 28 14 0.0275537
GO:0060099 regulation of phagocytosis, engulfment 7 6 0.0275537
GO:0065008 regulation of biological quality 2575 578 0.0277710
GO:0006793 phosphorus metabolic process 3268 726 0.0290675
GO:0002250 adaptive immune response 194 58 0.0290675
GO:0019725 cellular homeostasis 537 138 0.0291617
GO:0090382 phagosome maturation 42 18 0.0291686
GO:0061564 axon development 487 129 0.0291686
GO:0031349 positive regulation of defense response 259 74 0.0296274
GO:0051239 regulation of multicellular organismal process 1819 418 0.0306666
GO:0006778 porphyrin-containing compound metabolic process 35 16 0.0309914
GO:0048518 positive regulation of biological process 3684 808 0.0312992
GO:0006754 ATP biosynthetic process 36 16 0.0318428
GO:0009306 protein secretion 183 55 0.0327028
GO:0006950 response to stress 2909 645 0.0333036
GO:0045577 regulation of B cell differentiation 20 11 0.0334848
GO:0006796 phosphate-containing compound metabolic process 3226 716 0.0337566
GO:0070486 leukocyte aggregation 10 7 0.0376449
GO:0032496 response to lipopolysaccharide 200 59 0.0387517
GO:0043244 regulation of protein complex disassembly 77 28 0.0387830
GO:0007492 endoderm development 62 24 0.0387830
GO:0050855 regulation of B cell receptor signaling pathway 12 8 0.0397744
GO:0043623 cellular protein complex assembly 352 95 0.0397744
GO:0042116 macrophage activation 39 17 0.0404490
GO:0012501 programmed cell death 1539 356 0.0413113
GO:0002699 positive regulation of immune effector process 109 36 0.0413113
GO:0055082 cellular chemical homeostasis 433 113 0.0414985
GO:0006839 mitochondrial transport 169 51 0.0419163
GO:0006915 apoptotic process 1521 352 0.0419471
GO:0035556 intracellular signal transduction 1995 455 0.0426498
GO:0043303 mast cell degranulation 27 13 0.0449524
GO:0002237 response to molecule of bacterial origin 214 62 0.0464668
GO:0050871 positive regulation of B cell activation 50 20 0.0464668
GO:0050832 defense response to fungus 11 7 0.0464668
GO:0042168 heme metabolic process 27 13 0.0464668
GO:0046633 alpha-beta T cell proliferation 21 11 0.0484671
GO:0006873 cellular ion homeostasis 365 97 0.0485517
GO:0050708 regulation of protein secretion 134 42 0.0499129

Under enriched (60)

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
10619 GO:0016070 RNA metabolic process 3693 568 0.0000000
11977 GO:0090304 nucleic acid metabolic process 4166 655 0.0000000
12294 GO:0010467 gene expression 4322 696 0.0000000
12306 GO:0032774 RNA biosynthetic process 3063 483 0.0000000
12308 GO:0016071 mRNA metabolic process 615 60 0.0000000
12338 GO:0006139 nucleobase-containing compound metabolic process 5435 935 0.0000000
12343 GO:0034645 cellular macromolecule biosynthetic process 3920 646 0.0000000
12346 GO:1901360 organic cyclic compound metabolic process 5728 993 0.0000000
12646 GO:0046483 heterocycle metabolic process 5565 967 0.0000000
12647 GO:0034654 nucleobase-containing compound biosynthetic process 3350 544 0.0000000
12694 GO:0006396 RNA processing 676 73 0.0000000
12726 GO:0006725 cellular aromatic compound metabolic process 5569 969 0.0000000
10384 GO:0006807 nitrogen compound metabolic process 6075 1073 0.0000001
10437 GO:0009059 macromolecule biosynthetic process 4025 676 0.0000001
10997 GO:0034641 cellular nitrogen compound metabolic process 5755 1010 0.0000001
8661 GO:0006351 transcription, DNA-templated 2952 477 0.0000002
8660 GO:0051252 regulation of RNA metabolic process 2966 481 0.0000004
8662 GO:0042254 ribosome biogenesis 167 6 0.0000004
8659 GO:0006355 regulation of transcription, DNA-templated 2851 460 0.0000004
8658 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 513 0.0000006
8657 GO:2001141 regulation of RNA biosynthetic process 2888 469 0.0000009
8656 GO:1901362 organic cyclic compound biosynthetic process 3503 583 0.0000010
8655 GO:0010468 regulation of gene expression 3465 578 0.0000013
8654 GO:0019438 aromatic compound biosynthetic process 3410 567 0.0000014
8653 GO:0044271 cellular nitrogen compound biosynthetic process 3463 577 0.0000014
8650 GO:0018130 heterocycle biosynthetic process 3413 569 0.0000021
8648 GO:0044260 cellular macromolecule metabolic process 6484 1165 0.0000029
8649 GO:0022613 ribonucleoprotein complex biogenesis 280 22 0.0000064
8644 GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 625 0.0000103
8651 GO:0006364 rRNA processing 117 3 0.0000109
8652 GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 2 0.0000121
8642 GO:0010556 regulation of macromolecule biosynthetic process 3214 539 0.0000121
8647 GO:0016072 rRNA metabolic process 122 4 0.0000277
8641 GO:0051171 regulation of nitrogen compound metabolic process 3754 647 0.0000414
8646 GO:0072599 establishment of protein localization to endoplasmic reticulum 111 3 0.0000450
8640 GO:0031326 regulation of cellular biosynthetic process 3340 568 0.0000476
8645 GO:0045047 protein targeting to ER 110 3 0.0000522
8643 GO:0006613 cotranslational protein targeting to membrane 109 3 0.0000582
8639 GO:0009889 regulation of biosynthetic process 3367 574 0.0000582
8638 GO:0006397 mRNA processing 404 44 0.0001339
8636 GO:0044249 cellular biosynthetic process 4756 846 0.0002305
8634 GO:0043170 macromolecule metabolic process 7144 1317 0.0002394
8635 GO:0009058 biosynthetic process 4899 874 0.0002394
8637 GO:0008380 RNA splicing 332 34 0.0002802
8632 GO:1901576 organic substance biosynthetic process 4830 864 0.0004804
8633 GO:0034470 ncRNA processing 235 21 0.0008775
8626 GO:0044238 primary metabolic process 8725 1647 0.0019314
8630 GO:0000956 nuclear-transcribed mRNA catabolic process 184 15 0.0028460
8628 GO:0006402 mRNA catabolic process 196 17 0.0037862
8631 GO:0006415 translational termination 95 4 0.0041460
8629 GO:0070972 protein localization to endoplasmic reticulum 128 8 0.0045244
8627 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 7 0.0054331
8625 GO:0034660 ncRNA metabolic process 325 37 0.0056967
8624 GO:0006414 translational elongation 121 8 0.0124632
8619 GO:0071704 organic substance metabolic process 8974 1709 0.0133016
8623 GO:0019083 viral transcription 158 13 0.0153143
8620 GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 220 23 0.0229048
8621 GO:0000398 mRNA splicing, via spliceosome 220 23 0.0229048
8618 GO:0000375 RNA splicing, via transesterification reactions 225 24 0.0280963
8617 GO:0006401 RNA catabolic process 222 24 0.0478951

Negative Effect

Over enriched categories (110)

category term numInCat numDEInCat q.value
GO:0006414 translational elongation 121 78 0.0000000
GO:0006415 translational termination 95 67 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 71 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 71 0.0000000
GO:0045047 protein targeting to ER 110 71 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 71 0.0000000
GO:0006413 translational initiation 167 91 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 73 0.0000000
GO:0016070 RNA metabolic process 3693 875 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 72 0.0000000
GO:0090304 nucleic acid metabolic process 4166 958 0.0000000
GO:0010467 gene expression 4322 984 0.0000000
GO:0006612 protein targeting to membrane 171 84 0.0000000
GO:0034645 cellular macromolecule biosynthetic process 3920 901 0.0000000
GO:0032774 RNA biosynthetic process 3063 733 0.0000000
GO:0019083 viral transcription 158 77 0.0000000
GO:0009059 macromolecule biosynthetic process 4025 911 0.0000000
GO:0006402 mRNA catabolic process 196 88 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 84 0.0000000
GO:0019080 viral gene expression 168 78 0.0000000
GO:0018130 heterocycle biosynthetic process 3413 789 0.0000000
GO:1901362 organic cyclic compound biosynthetic process 3503 804 0.0000000
GO:0034654 nucleobase-containing compound biosynthetic process 3350 773 0.0000000
GO:0006412 translation 496 164 0.0000000
GO:0044033 multi-organism metabolic process 178 79 0.0000000
GO:0019438 aromatic compound biosynthetic process 3410 782 0.0000000
GO:0044271 cellular nitrogen compound biosynthetic process 3463 791 0.0000000
GO:0006401 RNA catabolic process 222 92 0.0000000
GO:0016071 mRNA metabolic process 615 192 0.0000000
GO:0044249 cellular biosynthetic process 4756 1034 0.0000000
GO:0043624 cellular protein complex disassembly 174 77 0.0000000
GO:0009058 biosynthetic process 4899 1058 0.0000000
GO:1901576 organic substance biosynthetic process 4830 1043 0.0000000
GO:0043241 protein complex disassembly 195 82 0.0000000
GO:0090150 establishment of protein localization to membrane 296 108 0.0000000
GO:0022613 ribonucleoprotein complex biogenesis 280 104 0.0000000
GO:0044260 cellular macromolecule metabolic process 6484 1345 0.0000000
GO:0032984 macromolecular complex disassembly 205 82 0.0000000
GO:0046483 heterocycle metabolic process 5565 1170 0.0000000
GO:1901360 organic cyclic compound metabolic process 5728 1199 0.0000000
GO:0006807 nitrogen compound metabolic process 6075 1261 0.0000000
GO:0034641 cellular nitrogen compound metabolic process 5755 1201 0.0000000
GO:0043170 macromolecule metabolic process 7144 1451 0.0000000
GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 706 0.0000000
GO:0006139 nucleobase-containing compound metabolic process 5435 1141 0.0000000
GO:0042254 ribosome biogenesis 167 69 0.0000000
GO:0006725 cellular aromatic compound metabolic process 5569 1161 0.0000000
GO:0010556 regulation of macromolecule biosynthetic process 3214 716 0.0000000
GO:0006351 transcription, DNA-templated 2952 665 0.0000000
GO:0019058 viral life cycle 303 102 0.0000000
GO:0010468 regulation of gene expression 3465 763 0.0000000
GO:0072657 protein localization to membrane 371 117 0.0000000
GO:0072594 establishment of protein localization to organelle 456 137 0.0000000
GO:0031326 regulation of cellular biosynthetic process 3340 732 0.0000000
GO:0009889 regulation of biosynthetic process 3367 736 0.0000000
GO:0051252 regulation of RNA metabolic process 2966 658 0.0000000
GO:0006355 regulation of transcription, DNA-templated 2851 635 0.0000000
GO:2001141 regulation of RNA biosynthetic process 2888 639 0.0000000
GO:1902578 single-organism localization 426 127 0.0000000
GO:1902580 single-organism cellular localization 426 127 0.0000000
GO:0044237 cellular metabolic process 8652 1689 0.0000001
GO:0006396 RNA processing 676 182 0.0000001
GO:0006605 protein targeting 497 142 0.0000001
GO:0016072 rRNA metabolic process 122 50 0.0000001
GO:0044238 primary metabolic process 8725 1699 0.0000003
GO:0071704 organic substance metabolic process 8974 1742 0.0000003
GO:0006364 rRNA processing 117 48 0.0000003
GO:0033365 protein localization to organelle 603 160 0.0000030
GO:0022411 cellular component disassembly 412 118 0.0000038
GO:0044802 single-organism membrane organization 638 167 0.0000042
GO:0016482 cytoplasmic transport 825 207 0.0000045
GO:0060255 regulation of macromolecule metabolic process 4402 905 0.0000069
GO:0042274 ribosomal small subunit biogenesis 21 15 0.0000077
GO:0008152 metabolic process 9725 1855 0.0000097
GO:0061024 membrane organization 778 193 0.0000258
GO:0044764 multi-organism cellular process 682 171 0.0000404
GO:0016032 viral process 674 169 0.0000454
GO:0080090 regulation of primary metabolic process 4733 961 0.0000749
GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 763 0.0000788
GO:0006417 regulation of translation 249 76 0.0000944
GO:0006886 intracellular protein transport 758 186 0.0001585
GO:0031323 regulation of cellular metabolic process 4749 960 0.0003521
GO:0051171 regulation of nitrogen compound metabolic process 3754 774 0.0004761
GO:0044265 cellular macromolecule catabolic process 798 192 0.0007244
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 174 0.0012354
GO:0044419 interspecies interaction between organisms 727 174 0.0012354
GO:0009057 macromolecule catabolic process 983 228 0.0017525
GO:0034660 ncRNA metabolic process 325 87 0.0023183
GO:0022618 ribonucleoprotein complex assembly 135 44 0.0030731
GO:0008380 RNA splicing 332 89 0.0038200
GO:0034470 ncRNA processing 235 66 0.0045015
GO:0001731 formation of translation preinitiation complex 18 11 0.0066933
GO:0019222 regulation of metabolic process 5252 1038 0.0069030
GO:0071826 ribonucleoprotein complex subunit organization 141 44 0.0095243
GO:0046907 intracellular transport 1406 306 0.0107365
GO:0030490 maturation of SSU-rRNA 11 8 0.0107365
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 220 62 0.0113182
GO:0000398 mRNA splicing, via spliceosome 220 62 0.0113182
GO:0000375 RNA splicing, via transesterification reactions 225 63 0.0116822
GO:0070727 cellular macromolecule localization 1129 251 0.0136243
GO:0000028 ribosomal small subunit assembly 7 6 0.0157615
GO:0071702 organic substance transport 1993 417 0.0180100
GO:0034613 cellular protein localization 1124 249 0.0180100
GO:0043933 macromolecular complex subunit organization 1450 312 0.0189400
GO:1902582 single-organism intracellular transport 1181 257 0.0319628
GO:0033036 macromolecule localization 2032 423 0.0369657
GO:0010746 regulation of plasma membrane long-chain fatty acid transport 5 5 0.0369657
GO:0006397 mRNA processing 404 100 0.0421020
GO:0042273 ribosomal large subunit biogenesis 16 9 0.0422356
GO:0015931 nucleobase-containing compound transport 169 49 0.0494171

Under enriched (68)

category term numInCat numDEInCat q.value2
7843 GO:0002376 immune system process 1936 257 0.0000550
7842 GO:0050896 response to stimulus 6126 973 0.0000605
7840 GO:0007165 signal transduction 4077 624 0.0000775
7841 GO:0006955 immune response 1137 136 0.0000775
7838 GO:0023052 signaling 4496 699 0.0000920
7839 GO:0044700 single organism signaling 4496 699 0.0000920
7837 GO:0007154 cell communication 4559 713 0.0001813
7836 GO:0007166 cell surface receptor signaling pathway 2374 344 0.0003972
7835 GO:0042060 wound healing 595 66 0.0010302
7834 GO:0040011 locomotion 1247 166 0.0010302
7832 GO:0009605 response to external stimulus 1589 221 0.0032541
7830 GO:0051716 cellular response to stimulus 4976 798 0.0032541
7833 GO:0001775 cell activation 767 92 0.0032541
7831 GO:0006952 defense response 1178 153 0.0032541
7827 GO:0044763 single-organism cellular process 9511 1613 0.0036668
7829 GO:0002682 regulation of immune system process 997 127 0.0036668
7828 GO:0009611 response to wounding 833 104 0.0036668
7825 GO:0048870 cell motility 948 123 0.0038317
7826 GO:0051674 localization of cell 948 123 0.0038317
7823 GO:0016477 cell migration 887 114 0.0046988
7821 GO:0006928 cellular component movement 1405 198 0.0046988
7818 GO:0048583 regulation of response to stimulus 2704 413 0.0056065
7822 GO:0016337 single organismal cell-cell adhesion 283 26 0.0069373
7820 GO:0050900 leukocyte migration 271 23 0.0078081
7819 GO:0001525 angiogenesis 350 35 0.0078081
7817 GO:0045321 leukocyte activation 561 64 0.0082175
7814 GO:0048646 anatomical structure formation involved in morphogenesis 855 112 0.0082189
7816 GO:0007599 hemostasis 485 55 0.0085027
7813 GO:0050817 coagulation 483 55 0.0095997
7811 GO:0050776 regulation of immune response 666 81 0.0114661
7812 GO:0007596 blood coagulation 480 55 0.0114661
7810 GO:0007186 G-protein coupled receptor signaling pathway 549 63 0.0114661
7806 GO:0044699 single-organism process 10471 1798 0.0142149
7804 GO:0006950 response to stress 2909 448 0.0148080
7809 GO:0042110 T cell activation 347 35 0.0148916
7802 GO:0009117 nucleotide metabolic process 1456 211 0.0164714
7803 GO:0045087 innate immune response 724 91 0.0169387
7800 GO:0006753 nucleoside phosphate metabolic process 1461 212 0.0169387
7808 GO:0098602 single organism cell adhesion 327 34 0.0171181
7798 GO:0044707 single-multicellular organism process 4822 786 0.0171181
7824 GO:0050868 negative regulation of T cell activation 64 1 0.0197323
7795 GO:0032501 multicellular organismal process 4965 812 0.0198891
7815 GO:0051250 negative regulation of lymphocyte activation 86 3 0.0198891
7799 GO:0046649 lymphocyte activation 480 55 0.0221414
7796 GO:0022610 biological adhesion 916 126 0.0221414
7793 GO:0055086 nucleobase-containing small molecule metabolic process 1507 221 0.0221414
7797 GO:0048514 blood vessel morphogenesis 421 48 0.0221414
7792 GO:0007155 cell adhesion 912 126 0.0271365
7787 GO:0006163 purine nucleotide metabolic process 1313 191 0.0284675
7807 GO:0002695 negative regulation of leukocyte activation 102 5 0.0284675
9404 GO:0032945 negative regulation of mononuclear cell proliferation 47 0 0.0284675
10063 GO:0050672 negative regulation of lymphocyte proliferation 47 0 0.0284675
7790 GO:0001944 vasculature development 509 62 0.0284675
7784 GO:0035556 intracellular signal transduction 1995 304 0.0284675
7788 GO:0006935 chemotaxis 558 69 0.0284675
7789 GO:0042330 taxis 558 69 0.0284675
7785 GO:0019693 ribose phosphate metabolic process 1311 191 0.0284675
7805 GO:0007187 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger 100 5 0.0295986
7801 GO:0050866 negative regulation of cell activation 110 6 0.0300774
7780 GO:0009259 ribonucleotide metabolic process 1307 191 0.0324804
7783 GO:0050878 regulation of body fluid levels 579 73 0.0326115
7778 GO:0009150 purine ribonucleotide metabolic process 1292 189 0.0358896
7782 GO:0002694 regulation of leukocyte activation 340 36 0.0377576
7779 GO:0050865 regulation of cell activation 366 40 0.0435802
7776 GO:0043207 response to external biotic stimulus 535 64 0.0437917
7777 GO:0051707 response to other organism 535 64 0.0437917
7775 GO:0001568 blood vessel development 480 59 0.0443171
7786 GO:0045165 cell fate commitment 172 14 0.0443171

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)