This report has goseq results for fasting insulin when:

  1. Genes with FDR < 0.05 marked as differentially expressed
  2. Only above genes with positive effect marked as differentially expressed
  3. Only genes from 1 with negative effect marked as differentially expressed

This report was generated on June 15 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_all_genes.txt"
outFile <- "S_Insu2"

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 genes with FDR < 0.1 as differentially expressed. The second and third vectors mark the genes with positive or negative effect in this list as differentially expressed.

genes <- as.numeric(data$q.value <= 0.05)
genesPos <- as.numeric(data$q.value <= 0.05 & data$effect > 0)
genesNeg <- as.numeric(data$q.value <= 0.05 & data$effect < 0)

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

There are 3262 DE genes with postive effect and 2818 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

FDR < 0.05

Over enriched categories (112)

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:0006415 translational termination 95 75 0.0000000
GO:0006414 translational elongation 121 89 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 81 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 82 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 83 0.0000000
GO:0045047 protein targeting to ER 110 82 0.0000000
GO:0006413 translational initiation 167 110 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 90 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 85 0.0000000
GO:0006612 protein targeting to membrane 171 106 0.0000000
GO:0019083 viral transcription 158 98 0.0000000
GO:0019080 viral gene expression 168 99 0.0000000
GO:0043624 cellular protein complex disassembly 174 102 0.0000000
GO:0043241 protein complex disassembly 195 111 0.0000000
GO:0044033 multi-organism metabolic process 178 102 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 105 0.0000000
GO:0032984 macromolecular complex disassembly 205 113 0.0000000
GO:0006412 translation 496 230 0.0000000
GO:0006401 RNA catabolic process 222 120 0.0000000
GO:0006402 mRNA catabolic process 196 108 0.0000000
GO:0046649 lymphocyte activation 480 223 0.0000000
GO:0045321 leukocyte activation 561 252 0.0000000
GO:0090150 establishment of protein localization to membrane 296 145 0.0000002
GO:0002757 immune response-activating signal transduction 333 162 0.0000002
GO:0022411 cellular component disassembly 412 192 0.0000002
GO:0043933 macromolecular complex subunit organization 1450 573 0.0000003
GO:0071822 protein complex subunit organization 1283 512 0.0000005
GO:0006955 immune response 1137 454 0.0000008
GO:1902578 single-organism localization 426 194 0.0000010
GO:1902580 single-organism cellular localization 426 194 0.0000010
GO:0016482 cytoplasmic transport 825 344 0.0000011
GO:0072594 establishment of protein localization to organelle 456 204 0.0000019
GO:0072657 protein localization to membrane 371 171 0.0000020
GO:0019058 viral life cycle 303 143 0.0000026
GO:0001775 cell activation 767 319 0.0000033
GO:0002253 activation of immune response 373 171 0.0000081
GO:0006605 protein targeting 497 217 0.0000084
GO:0042113 B cell activation 169 89 0.0000133
GO:0044267 cellular protein metabolic process 3491 1263 0.0000235
GO:0033365 protein localization to organelle 603 254 0.0000263
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 298 0.0000288
GO:0044419 interspecies interaction between organisms 727 298 0.0000288
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 102 0.0000288
GO:0042110 T cell activation 347 157 0.0000336
GO:0002376 immune system process 1936 722 0.0000337
GO:0070727 cellular macromolecule localization 1129 444 0.0000388
GO:0044764 multi-organism cellular process 682 281 0.0000394
GO:1902582 single-organism intracellular transport 1181 461 0.0000403
GO:0002764 immune response-regulating signaling pathway 428 189 0.0000437
GO:0044802 single-organism membrane organization 638 265 0.0000437
GO:0050778 positive regulation of immune response 441 192 0.0000510
GO:0016032 viral process 674 277 0.0000535
GO:0033036 macromolecule localization 2032 758 0.0000541
GO:0061024 membrane organization 778 315 0.0000609
GO:0034613 cellular protein localization 1124 440 0.0000649
GO:0002684 positive regulation of immune system process 610 253 0.0000660
GO:0006886 intracellular protein transport 758 307 0.0000996
GO:0042100 B cell proliferation 57 36 0.0002886
GO:0051249 regulation of lymphocyte activation 298 134 0.0003310
GO:0019538 protein metabolic process 4128 1463 0.0006765
GO:0050851 antigen receptor-mediated signaling pathway 138 71 0.0007143
GO:0045087 innate immune response 724 290 0.0007219
GO:0030098 lymphocyte differentiation 235 109 0.0011867
GO:0050776 regulation of immune response 666 268 0.0017712
GO:0002682 regulation of immune system process 997 385 0.0018173
GO:0008104 protein localization 1760 654 0.0019064
GO:0046651 lymphocyte proliferation 189 89 0.0019459
GO:0002694 regulation of leukocyte activation 340 146 0.0031000
GO:0032943 mononuclear cell proliferation 191 89 0.0032373
GO:0051251 positive regulation of lymphocyte activation 212 97 0.0037675
GO:0046907 intracellular transport 1406 527 0.0044983
GO:0030217 T cell differentiation 167 80 0.0053596
GO:0002696 positive regulation of leukocyte activation 230 103 0.0056115
GO:0050830 defense response to Gram-positive bacterium 38 24 0.0063380
GO:0050867 positive regulation of cell activation 239 106 0.0069964
GO:0098542 defense response to other organism 271 117 0.0077500
GO:0030888 regulation of B cell proliferation 46 28 0.0087630
GO:0006417 regulation of translation 249 111 0.0093896
GO:0002252 immune effector process 504 203 0.0094980
GO:0050865 regulation of cell activation 366 153 0.0098798
GO:0002758 innate immune response-activating signal transduction 160 76 0.0117541
GO:0031294 lymphocyte costimulation 63 35 0.0121988
GO:0031295 T cell costimulation 63 35 0.0121988
GO:0070661 leukocyte proliferation 200 90 0.0124528
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 134 0.0140673
GO:0015031 protein transport 1320 491 0.0154782
GO:0050864 regulation of B cell activation 82 43 0.0163602
GO:0002218 activation of innate immune response 167 78 0.0169027
GO:0043207 response to external biotic stimulus 535 211 0.0171432
GO:0051707 response to other organism 535 211 0.0171432
GO:0065003 macromolecular complex assembly 1091 410 0.0179169
GO:0050863 regulation of T cell activation 226 99 0.0188985
GO:0050871 positive regulation of B cell activation 50 29 0.0189268
GO:0002274 myeloid leukocyte activation 123 59 0.0213655
GO:0002221 pattern recognition receptor signaling pathway 158 74 0.0216628
GO:0002521 leukocyte differentiation 353 147 0.0231328
GO:0009607 response to biotic stimulus 566 221 0.0231495
GO:0044265 cellular macromolecule catabolic process 798 307 0.0245429
GO:0042274 ribosomal small subunit biogenesis 21 15 0.0249248
GO:0002224 toll-like receptor signaling pathway 136 65 0.0249248
GO:0002263 cell activation involved in immune response 141 66 0.0249248
GO:0002366 leukocyte activation involved in immune response 141 66 0.0249248
GO:0045184 establishment of protein localization 1422 523 0.0291588
GO:0051641 cellular localization 2267 812 0.0293642
GO:0001816 cytokine production 471 187 0.0300089
GO:0031663 lipopolysaccharide-mediated signaling pathway 45 26 0.0315109
GO:0000028 ribosomal small subunit assembly 7 7 0.0363057
GO:0071216 cellular response to biotic stimulus 125 59 0.0391391
GO:0002831 regulation of response to biotic stimulus 97 48 0.0423343
GO:0045089 positive regulation of innate immune response 196 87 0.0443445
GO:0030097 hemopoiesis 587 230 0.0474522
GO:0032615 interleukin-12 production 41 24 0.0474522

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
9740 GO:0051148 negative regulation of muscle cell differentiation 35 2 1
9739 GO:0007588 excretion 42 4 1
11536 GO:0051180 vitamin transport 18 0 1
11782 GO:0072012 glomerulus vasculature development 17 0 1
9738 GO:0050679 positive regulation of epithelial cell proliferation 123 25 1
11534 GO:0051154 negative regulation of striated muscle cell differentiation 15 0 1
9731 GO:0045165 cell fate commitment 172 39 1
9736 GO:0055013 cardiac muscle cell development 47 7 1
9724 GO:0007399 nervous system development 1658 498 1
9728 GO:0007224 smoothened signaling pathway 105 22 1
9737 GO:0019933 cAMP-mediated signaling 35 4 1
11019 GO:0014821 phasic smooth muscle contraction 14 0 1
9735 GO:0032330 regulation of chondrocyte differentiation 38 5 1
9725 GO:0002064 epithelial cell development 156 36 1
9730 GO:0001938 positive regulation of endothelial cell proliferation 60 10 1
11614 GO:0060442 branching involved in prostate gland morphogenesis 13 0 1
9733 GO:0019935 cyclic-nucleotide-mediated signaling 43 6 1
9709 GO:0009792 embryo development ending in birth or egg hatching 530 147 1
9701 GO:0007267 cell-cell signaling 915 263 1
9732 GO:0048663 neuron fate commitment 38 5 1

Positive Effect

Over enriched categories (238)

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:0045321 leukocyte activation 561 198 0.0000000
GO:0002376 immune system process 1936 512 0.0000000
GO:0006955 immune response 1137 333 0.0000000
GO:0046649 lymphocyte activation 480 173 0.0000000
GO:0001775 cell activation 767 243 0.0000000
GO:0002757 immune response-activating signal transduction 333 125 0.0000000
GO:0042110 T cell activation 347 127 0.0000000
GO:0002682 regulation of immune system process 997 279 0.0000000
GO:0002253 activation of immune response 373 130 0.0000000
GO:0002684 positive regulation of immune system process 610 187 0.0000000
GO:0050776 regulation of immune response 666 200 0.0000000
GO:0050778 positive regulation of immune response 441 145 0.0000000
GO:0045087 innate immune response 724 209 0.0000000
GO:0006952 defense response 1178 303 0.0000000
GO:0002764 immune response-regulating signaling pathway 428 137 0.0000000
GO:0051249 regulation of lymphocyte activation 298 103 0.0000000
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 79 0.0000000
GO:0050900 leukocyte migration 271 94 0.0000000
GO:0002694 regulation of leukocyte activation 340 112 0.0000000
GO:0002252 immune effector process 504 150 0.0000000
GO:0042113 B cell activation 169 67 0.0000000
GO:0043207 response to external biotic stimulus 535 156 0.0000000
GO:0051707 response to other organism 535 156 0.0000000
GO:0050865 regulation of cell activation 366 117 0.0000000
GO:0009607 response to biotic stimulus 566 162 0.0000001
GO:0046651 lymphocyte proliferation 189 71 0.0000001
GO:0032943 mononuclear cell proliferation 191 71 0.0000001
GO:0050851 antigen receptor-mediated signaling pathway 138 57 0.0000001
GO:0098542 defense response to other organism 271 90 0.0000002
GO:0050863 regulation of T cell activation 226 79 0.0000003
GO:0002274 myeloid leukocyte activation 123 51 0.0000004
GO:0030098 lymphocyte differentiation 235 81 0.0000007
GO:0070661 leukocyte proliferation 200 71 0.0000008
GO:0002696 positive regulation of leukocyte activation 230 78 0.0000013
GO:0001816 cytokine production 471 135 0.0000014
GO:0050867 positive regulation of cell activation 239 80 0.0000015
GO:0051251 positive regulation of lymphocyte activation 212 73 0.0000019
GO:0022904 respiratory electron transport chain 105 43 0.0000021
GO:0002521 leukocyte differentiation 353 108 0.0000021
GO:0022900 electron transport chain 106 43 0.0000028
GO:0050896 response to stimulus 6126 1247 0.0000040
GO:0002263 cell activation involved in immune response 141 54 0.0000040
GO:0002366 leukocyte activation involved in immune response 141 54 0.0000040
GO:0030217 T cell differentiation 167 61 0.0000073
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 95 0.0000236
GO:0042100 B cell proliferation 57 28 0.0000266
GO:0050670 regulation of lymphocyte proliferation 146 53 0.0000310
GO:0050870 positive regulation of T cell activation 165 58 0.0000330
GO:0072676 lymphocyte migration 47 24 0.0000345
GO:0006950 response to stress 2909 625 0.0000356
GO:0032944 regulation of mononuclear cell proliferation 147 53 0.0000374
GO:0007165 signal transduction 4077 852 0.0000499
GO:0001817 regulation of cytokine production 417 116 0.0000561
GO:0031294 lymphocyte costimulation 63 29 0.0000561
GO:0031295 T cell costimulation 63 29 0.0000561
GO:0045088 regulation of innate immune response 243 77 0.0000561
GO:0070663 regulation of leukocyte proliferation 151 53 0.0000909
GO:0031347 regulation of defense response 462 125 0.0001321
GO:0030595 leukocyte chemotaxis 130 46 0.0001548
GO:0050853 B cell receptor signaling pathway 39 21 0.0001665
GO:0044763 single-organism cellular process 9511 1852 0.0001753
GO:0042098 T cell proliferation 135 48 0.0001875
GO:0002831 regulation of response to biotic stimulus 97 38 0.0002459
GO:0009617 response to bacterium 298 86 0.0002663
GO:0032615 interleukin-12 production 41 21 0.0002916
GO:0045333 cellular respiration 158 52 0.0003399
GO:0048584 positive regulation of response to stimulus 1324 306 0.0003774
GO:0050852 T cell receptor signaling pathway 106 40 0.0004154
GO:0002218 activation of innate immune response 167 56 0.0004609
GO:0050864 regulation of B cell activation 82 33 0.0004828
GO:0009620 response to fungus 23 14 0.0005285
GO:0002758 innate immune response-activating signal transduction 160 54 0.0005491
GO:0002443 leukocyte mediated immunity 211 65 0.0005741
GO:0060326 cell chemotaxis 177 56 0.0005938
GO:0032655 regulation of interleukin-12 production 40 20 0.0007158
GO:0009615 response to virus 261 77 0.0007944
GO:0042129 regulation of T cell proliferation 108 39 0.0008925
GO:0048518 positive regulation of biological process 3684 767 0.0009301
GO:0045089 positive regulation of innate immune response 196 62 0.0009939
GO:0002275 myeloid cell activation involved in immune response 54 24 0.0010283
GO:0048583 regulation of response to stimulus 2704 578 0.0011983
GO:0042742 defense response to bacterium 102 36 0.0011983
GO:0002697 regulation of immune effector process 231 69 0.0014423
GO:0007599 hemostasis 485 127 0.0015636
GO:0002221 pattern recognition receptor signaling pathway 158 52 0.0015636
GO:0007005 mitochondrion organization 298 84 0.0015636
GO:0002520 immune system development 648 162 0.0016562
GO:0007154 cell communication 4559 932 0.0017470
GO:0035987 endodermal cell differentiation 38 19 0.0017639
GO:0023052 signaling 4496 920 0.0017785
GO:0044700 single organism signaling 4496 920 0.0017785
GO:0050817 coagulation 483 126 0.0019921
GO:0006119 oxidative phosphorylation 70 27 0.0020623
GO:0007596 blood coagulation 480 125 0.0022809
GO:0050830 defense response to Gram-positive bacterium 38 18 0.0022848
GO:0030097 hemopoiesis 587 148 0.0023031
GO:0002250 adaptive immune response 194 59 0.0023854
GO:0006909 phagocytosis 162 52 0.0024020
GO:0097529 myeloid leukocyte migration 104 36 0.0024321
GO:0001819 positive regulation of cytokine production 245 71 0.0025816
GO:0097530 granulocyte migration 71 27 0.0026626
GO:0009306 protein secretion 183 56 0.0029220
GO:0070271 protein complex biogenesis 934 219 0.0030298
GO:0031349 positive regulation of defense response 259 74 0.0031961
GO:0009605 response to external stimulus 1589 351 0.0031961
GO:1990266 neutrophil migration 57 23 0.0036143
GO:0050688 regulation of defense response to virus 71 28 0.0036606
GO:0050663 cytokine secretion 108 37 0.0039569
GO:0006968 cellular defense response 45 20 0.0039735
GO:0050854 regulation of antigen receptor-mediated signaling pathway 34 17 0.0039735
GO:0048247 lymphocyte chemotaxis 24 13 0.0040063
GO:0042102 positive regulation of T cell proliferation 70 27 0.0044523
GO:0048534 hematopoietic or lymphoid organ development 615 152 0.0046371
GO:0006461 protein complex assembly 932 217 0.0048661
GO:0051607 defense response to virus 173 53 0.0055117
GO:0030888 regulation of B cell proliferation 46 20 0.0067324
GO:0042060 wound healing 595 147 0.0067854
GO:0002237 response to molecule of bacterial origin 214 62 0.0072550
GO:0043299 leukocyte degranulation 43 19 0.0073686
GO:0070098 chemokine-mediated signaling pathway 37 17 0.0073686
GO:0030593 neutrophil chemotaxis 56 22 0.0074903
GO:0045576 mast cell activation 40 18 0.0075126
GO:0002444 myeloid leukocyte mediated immunity 54 22 0.0075522
GO:0007166 cell surface receptor signaling pathway 2374 504 0.0075522
GO:0046631 alpha-beta T cell activation 86 31 0.0077644
GO:0002224 toll-like receptor signaling pathway 136 44 0.0080220
GO:0006091 generation of precursor metabolites and energy 394 101 0.0081598
GO:0001706 endoderm formation 46 20 0.0084247
GO:0007159 leukocyte cell-cell adhesion 44 19 0.0094097
GO:0042773 ATP synthesis coupled electron transport 54 21 0.0094322
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 21 0.0094322
GO:0070665 positive regulation of leukocyte proliferation 100 34 0.0094322
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 34 0.0094322
GO:0036336 dendritic cell migration 22 12 0.0101527
GO:0034097 response to cytokine 534 132 0.0104598
GO:0050671 positive regulation of lymphocyte proliferation 97 33 0.0111206
GO:0044699 single-organism process 10471 2001 0.0111799
GO:0050707 regulation of cytokine secretion 90 31 0.0112633
GO:1902105 regulation of leukocyte differentiation 178 53 0.0113817
GO:0001774 microglial cell activation 11 8 0.0115644
GO:0009611 response to wounding 833 194 0.0116990
GO:0045055 regulated secretory pathway 55 22 0.0117047
GO:0043900 regulation of multi-organism process 273 74 0.0117395
GO:0048522 positive regulation of cellular process 3307 680 0.0129805
GO:0032946 positive regulation of mononuclear cell proliferation 98 33 0.0131572
GO:0006839 mitochondrial transport 169 50 0.0134151
GO:0010033 response to organic substance 2043 435 0.0137016
GO:0071621 granulocyte chemotaxis 67 24 0.0141592
GO:0002431 Fc receptor mediated stimulatory signaling pathway 73 27 0.0141841
GO:0051716 cellular response to stimulus 4976 995 0.0146001
GO:0065003 macromolecular complex assembly 1091 245 0.0151340
GO:0002440 production of molecular mediator of immune response 103 34 0.0154174
GO:0030889 negative regulation of B cell proliferation 14 9 0.0162141
GO:0032496 response to lipopolysaccharide 200 57 0.0166557
GO:0072593 reactive oxygen species metabolic process 133 41 0.0168915
GO:0008089 anterograde axon cargo transport 23 12 0.0173180
GO:0002683 negative regulation of immune system process 198 57 0.0177627
GO:0006915 apoptotic process 1521 330 0.0182385
GO:0033630 positive regulation of cell adhesion mediated by integrin 15 9 0.0190754
GO:0045577 regulation of B cell differentiation 20 11 0.0193415
GO:0050871 positive regulation of B cell activation 50 20 0.0194876
GO:0002820 negative regulation of adaptive immune response 17 10 0.0197201
GO:0050777 negative regulation of immune response 60 23 0.0198405
GO:0012501 programmed cell death 1539 333 0.0203027
GO:0002282 microglial cell activation involved in immune response 7 6 0.0204910
GO:0019221 cytokine-mediated signaling pathway 345 89 0.0216649
GO:0032945 negative regulation of mononuclear cell proliferation 47 19 0.0216649
GO:0050672 negative regulation of lymphocyte proliferation 47 19 0.0216649
GO:0042221 response to chemical 2788 575 0.0216649
GO:0032609 interferon-gamma production 78 27 0.0218785
GO:0015671 oxygen transport 11 7 0.0218785
GO:0002407 dendritic cell chemotaxis 18 10 0.0220880
GO:2000401 regulation of lymphocyte migration 28 13 0.0222176
GO:0032735 positive regulation of interleukin-12 production 21 11 0.0231878
GO:0045619 regulation of lymphocyte differentiation 104 34 0.0233606
GO:0052564 response to immune response of other organism involved in symbiotic interaction 12 8 0.0252250
GO:0052572 response to host immune response 12 8 0.0252250
GO:0033014 tetrapyrrole biosynthetic process 30 14 0.0256763
GO:0050855 regulation of B cell receptor signaling pathway 12 8 0.0257376
GO:0032755 positive regulation of interleukin-6 production 34 15 0.0257376
GO:0006911 phagocytosis, engulfment 21 11 0.0261769
GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I 79 27 0.0262755
GO:0046633 alpha-beta T cell proliferation 21 11 0.0269132
GO:0002704 negative regulation of leukocyte mediated immunity 18 10 0.0274165
GO:0050832 defense response to fungus 11 7 0.0276539
GO:0031663 lipopolysaccharide-mediated signaling pathway 45 18 0.0277957
GO:0006954 inflammatory response 473 114 0.0277957
GO:0086011 membrane repolarization during action potential 10 7 0.0277957
GO:0002433 immune response-regulating cell surface receptor signaling pathway involved in phagocytosis 69 25 0.0294009
GO:0038094 Fc-gamma receptor signaling pathway 69 25 0.0294009
GO:0038096 Fc-gamma receptor signaling pathway involved in phagocytosis 69 25 0.0294009
GO:0051250 negative regulation of lymphocyte activation 86 29 0.0297542
GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 172 49 0.0306093
GO:0007492 endoderm development 62 23 0.0314747
GO:0071345 cellular response to cytokine stimulus 452 111 0.0314747
GO:0036230 granulocyte activation 25 12 0.0322040
GO:0002448 mast cell mediated immunity 28 13 0.0322040
GO:0034109 homotypic cell-cell adhesion 68 24 0.0340317
GO:0050708 regulation of protein secretion 134 40 0.0354573
GO:0042119 neutrophil activation 22 11 0.0355576
GO:0032494 response to peptidoglycan 10 7 0.0365281
GO:0045785 positive regulation of cell adhesion 149 44 0.0366162
GO:0006457 protein folding 197 55 0.0367576
GO:0032101 regulation of response to external stimulus 501 120 0.0368041
GO:0002703 regulation of leukocyte mediated immunity 109 34 0.0380033
GO:0007229 integrin-mediated signaling pathway 86 29 0.0382706
GO:0002281 macrophage activation involved in immune response 13 8 0.0382977
GO:0071216 cellular response to biotic stimulus 125 38 0.0402068
GO:0002507 tolerance induction 16 9 0.0402394
GO:0050690 regulation of defense response to virus by virus 28 13 0.0405061
GO:0015949 nucleobase-containing small molecule interconversion 19 10 0.0409321
GO:0006928 cellular component movement 1405 304 0.0411141
GO:0072678 T cell migration 30 13 0.0414699
GO:0071219 cellular response to molecule of bacterial origin 109 34 0.0425346
GO:0070664 negative regulation of leukocyte proliferation 50 19 0.0426053
GO:0051701 interaction with host 105 33 0.0434509
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 16 0.0438230
GO:0052173 response to defenses of other organism involved in symbiotic interaction 13 8 0.0444267
GO:0052200 response to host defenses 13 8 0.0444267
GO:0075136 response to host 13 8 0.0444267
GO:0050857 positive regulation of antigen receptor-mediated signaling pathway 13 8 0.0445878
GO:0002707 negative regulation of lymphocyte mediated immunity 16 9 0.0445878
GO:0070887 cellular response to chemical stimulus 1926 404 0.0445878
GO:0042116 macrophage activation 39 16 0.0454480
GO:0002285 lymphocyte activation involved in immune response 89 29 0.0454480
GO:0002685 regulation of leukocyte migration 100 31 0.0454480
GO:0006935 chemotaxis 558 131 0.0454480
GO:0042330 taxis 558 131 0.0454480
GO:0052031 modulation by symbiont of host defense response 8 6 0.0454480
GO:0052255 modulation by organism of defense response of other organism involved in symbiotic interaction 8 6 0.0454480
GO:0052509 positive regulation by symbiont of host defense response 8 6 0.0454480
GO:0052510 positive regulation by organism of defense response of other organism involved in symbiotic interaction 8 6 0.0454480
GO:0052552 modulation by organism of immune response of other organism involved in symbiotic interaction 8 6 0.0454480
GO:0052553 modulation by symbiont of host immune response 8 6 0.0454480
GO:0032648 regulation of interferon-beta production 35 15 0.0463959
GO:0034622 cellular macromolecular complex assembly 583 136 0.0468116
GO:0046634 regulation of alpha-beta T cell activation 54 20 0.0468777
GO:0042981 regulation of apoptotic process 1145 250 0.0493168

Under enriched (26)

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
8329 GO:0016070 RNA metabolic process 3693 561 0.0000145
8328 GO:0090304 nucleic acid metabolic process 4166 650 0.0000716
8327 GO:0034654 nucleobase-containing compound biosynthetic process 3350 515 0.0002300
8326 GO:0032774 RNA biosynthetic process 3063 466 0.0002300
8325 GO:0006139 nucleobase-containing compound metabolic process 5435 889 0.0008430
8324 GO:1901360 organic cyclic compound metabolic process 5728 942 0.0008430
8323 GO:1901362 organic cyclic compound biosynthetic process 3503 550 0.0010197
8322 GO:0010467 gene expression 4322 694 0.0010197
8321 GO:0019438 aromatic compound biosynthetic process 3410 535 0.0010197
8320 GO:0006355 regulation of transcription, DNA-templated 2851 440 0.0010197
8317 GO:0006807 nitrogen compound metabolic process 6075 1010 0.0010197
8319 GO:0018130 heterocycle biosynthetic process 3413 536 0.0010197
8316 GO:0006725 cellular aromatic compound metabolic process 5569 918 0.0010197
8318 GO:0051252 regulation of RNA metabolic process 2966 460 0.0010197
8315 GO:0044271 cellular nitrogen compound biosynthetic process 3463 545 0.0010197
8314 GO:0046483 heterocycle metabolic process 5565 918 0.0010197
8313 GO:0034641 cellular nitrogen compound metabolic process 5755 954 0.0014082
8312 GO:2001141 regulation of RNA biosynthetic process 2888 450 0.0021051
8311 GO:0006351 transcription, DNA-templated 2952 462 0.0025990
8309 GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 591 0.0050785
8308 GO:0034645 cellular macromolecule biosynthetic process 3920 637 0.0102805
8307 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 500 0.0123073
8306 GO:0010468 regulation of gene expression 3465 559 0.0127091
8310 GO:0007224 smoothened signaling pathway 105 5 0.0151611
8305 GO:0051171 regulation of nitrogen compound metabolic process 3754 614 0.0229993
8304 GO:0006396 RNA processing 676 88 0.0418539

Negative Effect

Over enriched categories (83)

category term numInCat numDEInCat q.value
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 74 0.0000000
GO:0006415 translational termination 95 69 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 75 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 74 0.0000000
GO:0045047 protein targeting to ER 110 74 0.0000000
GO:0006414 translational elongation 121 77 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 76 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 73 0.0000000
GO:0006413 translational initiation 167 83 0.0000000
GO:0019083 viral transcription 158 80 0.0000000
GO:0006612 protein targeting to membrane 171 84 0.0000000
GO:0019080 viral gene expression 168 80 0.0000000
GO:0044033 multi-organism metabolic process 178 80 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 80 0.0000000
GO:0043624 cellular protein complex disassembly 174 77 0.0000000
GO:0043241 protein complex disassembly 195 82 0.0000000
GO:0006402 mRNA catabolic process 196 82 0.0000000
GO:0006401 RNA catabolic process 222 88 0.0000000
GO:0032984 macromolecular complex disassembly 205 82 0.0000000
GO:0090150 establishment of protein localization to membrane 296 101 0.0000000
GO:0019058 viral life cycle 303 97 0.0000000
GO:0072657 protein localization to membrane 371 110 0.0000000
GO:0006412 translation 496 130 0.0000000
GO:0022411 cellular component disassembly 412 116 0.0000000
GO:1902578 single-organism localization 426 116 0.0000000
GO:1902580 single-organism cellular localization 426 116 0.0000000
GO:0016071 mRNA metabolic process 615 151 0.0000000
GO:0072594 establishment of protein localization to organelle 456 119 0.0000000
GO:0006605 protein targeting 497 126 0.0000000
GO:0016070 RNA metabolic process 3693 650 0.0000000
GO:0090304 nucleic acid metabolic process 4166 720 0.0000000
GO:0032774 RNA biosynthetic process 3063 551 0.0000000
GO:0022613 ribonucleoprotein complex biogenesis 280 79 0.0000000
GO:0044802 single-organism membrane organization 638 148 0.0000001
GO:0042254 ribosome biogenesis 167 54 0.0000001
GO:0018130 heterocycle biosynthetic process 3413 597 0.0000001
GO:1901362 organic cyclic compound biosynthetic process 3503 610 0.0000001
GO:0034645 cellular macromolecule biosynthetic process 3920 673 0.0000001
GO:0034654 nucleobase-containing compound biosynthetic process 3350 587 0.0000001
GO:0019438 aromatic compound biosynthetic process 3410 594 0.0000002
GO:0061024 membrane organization 778 170 0.0000003
GO:0044271 cellular nitrogen compound biosynthetic process 3463 601 0.0000003
GO:0033365 protein localization to organelle 603 138 0.0000004
GO:0010467 gene expression 4322 726 0.0000006
GO:0009059 macromolecule biosynthetic process 4025 681 0.0000009
GO:0044249 cellular biosynthetic process 4756 783 0.0000034
GO:0044260 cellular macromolecule metabolic process 6484 1037 0.0000036
GO:0009058 biosynthetic process 4899 803 0.0000036
GO:1901576 organic substance biosynthetic process 4830 793 0.0000036
GO:0042274 ribosomal small subunit biogenesis 21 14 0.0000040
GO:0016482 cytoplasmic transport 825 173 0.0000040
GO:0016032 viral process 674 145 0.0000040
GO:0044764 multi-organism cellular process 682 146 0.0000050
GO:0044265 cellular macromolecule catabolic process 798 166 0.0000132
GO:0006139 nucleobase-containing compound metabolic process 5435 880 0.0000214
GO:0006364 rRNA processing 117 38 0.0000223
GO:0034641 cellular nitrogen compound metabolic process 5755 925 0.0000223
GO:0043170 macromolecule metabolic process 7144 1122 0.0000232
GO:0016072 rRNA metabolic process 122 39 0.0000255
GO:0006807 nitrogen compound metabolic process 6075 970 0.0000264
GO:0046483 heterocycle metabolic process 5565 897 0.0000264
GO:1901360 organic cyclic compound metabolic process 5728 920 0.0000264
GO:0043933 macromolecular complex subunit organization 1450 272 0.0000313
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 149 0.0000386
GO:0044419 interspecies interaction between organisms 727 149 0.0000386
GO:0006886 intracellular protein transport 758 155 0.0000780
GO:0006725 cellular aromatic compound metabolic process 5569 893 0.0001657
GO:0009057 macromolecule catabolic process 983 192 0.0002543
GO:0070727 cellular macromolecule localization 1129 215 0.0006784
GO:0071822 protein complex subunit organization 1283 239 0.0008359
GO:0034613 cellular protein localization 1124 213 0.0010428
GO:0006396 RNA processing 676 134 0.0024488
GO:0044238 primary metabolic process 8725 1329 0.0029397
GO:0071704 organic substance metabolic process 8974 1362 0.0037672
GO:0000028 ribosomal small subunit assembly 7 6 0.0043466
GO:0044237 cellular metabolic process 8652 1313 0.0075372
GO:0033036 macromolecule localization 2032 349 0.0130277
GO:0030490 maturation of SSU-rRNA 11 7 0.0253695
GO:1902582 single-organism intracellular transport 1181 211 0.0263334
GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 513 0.0323543
GO:0044270 cellular nitrogen compound catabolic process 1407 251 0.0323543
GO:0001731 formation of translation preinitiation complex 18 9 0.0409951
GO:0046907 intracellular transport 1406 245 0.0493987

Under enriched (1)

category term numInCat numDEInCat q.value2
7090 GO:0002376 immune system process 1936 210 0.0479962
7088 GO:0019882 antigen processing and presentation 215 11 0.2241914
7089 GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 2 0.2594231
7085 GO:0048002 antigen processing and presentation of peptide antigen 180 9 0.2594231
7084 GO:0019884 antigen processing and presentation of exogenous antigen 167 8 0.2594231
7082 GO:0050900 leukocyte migration 271 18 0.2594231
7081 GO:0006952 defense response 1178 123 0.2594231
7083 GO:0002478 antigen processing and presentation of exogenous peptide antigen 165 8 0.2594231
7087 GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I 79 1 0.2594231
8468 GO:0006521 regulation of cellular amino acid metabolic process 59 0 0.2705402
7080 GO:0001775 cell activation 767 76 0.2721465
7086 GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent 76 1 0.2985568
7079 GO:0006955 immune response 1137 121 0.3200407
7078 GO:0009605 response to external stimulus 1589 182 0.3200407
7076 GO:0040011 locomotion 1247 143 0.3489543
7074 GO:0006928 cellular component movement 1405 165 0.3544089
7073 GO:0007599 hemostasis 485 46 0.3582076
7077 GO:0006887 exocytosis 286 23 0.3582076
7070 GO:0002682 regulation of immune system process 997 106 0.3582076
7075 GO:0016337 single organismal cell-cell adhesion 283 23 0.3582076

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)