This report has goseq results for 30 minute peptide 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_fS_C_pept_30_all_genes.txt"
outFile <- "pept_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 3517 DE genes with postive effect and 3286 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 (56)

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 85 0.0000000
GO:0006415 translational termination 95 70 0.0000000
GO:0006413 translational initiation 167 105 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 74 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 75 0.0000000
GO:0045047 protein targeting to ER 110 75 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 75 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 78 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 82 0.0000000
GO:0043624 cellular protein complex disassembly 174 103 0.0000001
GO:0006612 protein targeting to membrane 171 100 0.0000003
GO:0043241 protein complex disassembly 195 111 0.0000004
GO:0019083 viral transcription 158 92 0.0000013
GO:0032984 macromolecular complex disassembly 205 113 0.0000020
GO:0002757 immune response-activating signal transduction 333 170 0.0000042
GO:0019080 viral gene expression 168 95 0.0000049
GO:0006412 translation 496 233 0.0000117
GO:0044033 multi-organism metabolic process 178 98 0.0000173
GO:0002253 activation of immune response 373 181 0.0000847
GO:0050778 positive regulation of immune response 441 208 0.0000984
GO:0019058 viral life cycle 303 147 0.0002630
GO:0006401 RNA catabolic process 222 113 0.0003466
GO:0072657 protein localization to membrane 371 175 0.0004139
GO:0031294 lymphocyte costimulation 63 41 0.0006082
GO:0031295 T cell costimulation 63 41 0.0006082
GO:0043933 macromolecular complex subunit organization 1450 599 0.0007273
GO:0000956 nuclear-transcribed mRNA catabolic process 184 96 0.0007733
GO:0002684 positive regulation of immune system process 610 271 0.0007733
GO:0006402 mRNA catabolic process 196 101 0.0009356
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 105 0.0011131
GO:0071822 protein complex subunit organization 1283 533 0.0012278
GO:0050851 antigen receptor-mediated signaling pathway 138 76 0.0012278
GO:0002764 immune response-regulating signaling pathway 428 199 0.0012778
GO:0046649 lymphocyte activation 480 217 0.0024542
GO:0045321 leukocyte activation 561 249 0.0025548
GO:0050776 regulation of immune response 666 291 0.0030587
GO:0022411 cellular component disassembly 412 189 0.0031950
GO:1902578 single-organism localization 426 194 0.0032966
GO:1902580 single-organism cellular localization 426 194 0.0032966
GO:0090150 establishment of protein localization to membrane 296 140 0.0039098
GO:0006968 cellular defense response 45 30 0.0040571
GO:0006955 immune response 1137 469 0.0041152
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 311 0.0065041
GO:0044419 interspecies interaction between organisms 727 311 0.0065041
GO:0022613 ribonucleoprotein complex biogenesis 280 133 0.0065041
GO:0044764 multi-organism cellular process 682 292 0.0117311
GO:0006417 regulation of translation 249 120 0.0126608
GO:0042110 T cell activation 347 159 0.0126608
GO:0002831 regulation of response to biotic stimulus 97 54 0.0126608
GO:0050852 T cell receptor signaling pathway 106 58 0.0146911
GO:0016032 viral process 674 287 0.0194081
GO:0051251 positive regulation of lymphocyte activation 212 102 0.0222073
GO:0002696 positive regulation of leukocyte activation 230 109 0.0253121
GO:0061024 membrane organization 778 326 0.0338173
GO:0050867 positive regulation of cell activation 239 112 0.0351747
GO:0050870 positive regulation of T cell activation 165 81 0.0435555

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
10032 GO:0002088 lens development in camera-type eye 53 5 0.1007683
10025 GO:0098661 inorganic anion transmembrane transport 70 13 1.0000000
10024 GO:0045165 cell fate commitment 172 42 1.0000000
11520 GO:0050655 dermatan sulfate proteoglycan metabolic process 15 0 1.0000000
11771 GO:0060850 regulation of transcription involved in cell fate commitment 15 0 1.0000000
10022 GO:0048705 skeletal system morphogenesis 183 46 1.0000000
10031 GO:0070306 lens fiber cell differentiation 20 1 1.0000000
10021 GO:0048562 embryonic organ morphogenesis 224 59 1.0000000
10030 GO:0051905 establishment of pigment granule localization 20 1 1.0000000
11601 GO:0051930 regulation of sensory perception of pain 15 0 1.0000000
11602 GO:0051931 regulation of sensory perception 15 0 1.0000000
10029 GO:0002089 lens morphogenesis in camera-type eye 20 1 1.0000000
11517 GO:0050651 dermatan sulfate proteoglycan biosynthetic process 14 0 1.0000000
10018 GO:0007187 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger 100 22 1.0000000
10028 GO:0051904 pigment granule transport 19 1 1.0000000
10027 GO:0032401 establishment of melanosome localization 19 1 1.0000000
10020 GO:0032069 regulation of nuclease activity 71 14 1.0000000
10017 GO:0006987 activation of signaling protein activity involved in unfolded protein response 63 12 1.0000000
10019 GO:1902476 chloride transmembrane transport 59 11 1.0000000
11685 GO:0060442 branching involved in prostate gland morphogenesis 13 0 1.0000000

Positive Effect

Over enriched categories (220)

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 344 0.0000000
GO:0002376 immune system process 1936 517 0.0000000
GO:0045321 leukocyte activation 561 193 0.0000000
GO:0050776 regulation of immune response 666 220 0.0000000
GO:0002682 regulation of immune system process 997 295 0.0000000
GO:0046649 lymphocyte activation 480 167 0.0000000
GO:0002757 immune response-activating signal transduction 333 128 0.0000000
GO:0002684 positive regulation of immune system process 610 198 0.0000000
GO:0050778 positive regulation of immune response 441 155 0.0000000
GO:0001775 cell activation 767 236 0.0000000
GO:0042110 T cell activation 347 128 0.0000000
GO:0002253 activation of immune response 373 133 0.0000000
GO:0002764 immune response-regulating signaling pathway 428 146 0.0000000
GO:0050851 antigen receptor-mediated signaling pathway 138 63 0.0000000
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 82 0.0000000
GO:0002694 regulation of leukocyte activation 340 116 0.0000000
GO:0006935 chemotaxis 558 170 0.0000000
GO:0042330 taxis 558 170 0.0000000
GO:0006952 defense response 1178 311 0.0000000
GO:0051249 regulation of lymphocyte activation 298 104 0.0000000
GO:0045087 innate immune response 724 205 0.0000001
GO:0050900 leukocyte migration 271 94 0.0000002
GO:0050865 regulation of cell activation 366 119 0.0000002
GO:0031294 lymphocyte costimulation 63 34 0.0000002
GO:0031295 T cell costimulation 63 34 0.0000002
GO:0050863 regulation of T cell activation 226 82 0.0000002
GO:0044763 single-organism cellular process 9511 1969 0.0000002
GO:0050896 response to stimulus 6126 1318 0.0000003
GO:0002696 positive regulation of leukocyte activation 230 82 0.0000005
GO:0051251 positive regulation of lymphocyte activation 212 77 0.0000006
GO:0050867 positive regulation of cell activation 239 84 0.0000006
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 104 0.0000006
GO:0050870 positive regulation of T cell activation 165 64 0.0000009
GO:0050852 T cell receptor signaling pathway 106 47 0.0000013
GO:0044699 single-organism process 10471 2137 0.0000016
GO:0070661 leukocyte proliferation 200 72 0.0000025
GO:0006968 cellular defense response 45 26 0.0000025
GO:0007165 signal transduction 4077 903 0.0000043
GO:0032943 mononuclear cell proliferation 191 69 0.0000063
GO:0002252 immune effector process 504 145 0.0000079
GO:0046651 lymphocyte proliferation 189 68 0.0000090
GO:0006928 cellular component movement 1405 346 0.0000134
GO:0040011 locomotion 1247 310 0.0000209
GO:0072676 lymphocyte migration 47 25 0.0000219
GO:0022904 respiratory electron transport chain 105 42 0.0000302
GO:0060326 cell chemotaxis 177 62 0.0000347
GO:0022900 electron transport chain 106 42 0.0000406
GO:0048584 positive regulation of response to stimulus 1324 324 0.0000416
GO:0002274 myeloid leukocyte activation 123 48 0.0000439
GO:0030595 leukocyte chemotaxis 130 49 0.0000458
GO:0042113 B cell activation 169 61 0.0000473
GO:0023052 signaling 4496 975 0.0000496
GO:0044700 single organism signaling 4496 975 0.0000496
GO:0042098 T cell proliferation 135 51 0.0000563
GO:0050853 B cell receptor signaling pathway 39 22 0.0000792
GO:0043207 response to external biotic stimulus 535 146 0.0001030
GO:0051707 response to other organism 535 146 0.0001030
GO:0045333 cellular respiration 158 55 0.0001481
GO:0045088 regulation of innate immune response 243 78 0.0001744
GO:0007154 cell communication 4559 985 0.0002162
GO:0002704 negative regulation of leukocyte mediated immunity 18 13 0.0002868
GO:0002697 regulation of immune effector process 231 74 0.0002868
GO:0002831 regulation of response to biotic stimulus 97 39 0.0002941
GO:0048247 lymphocyte chemotaxis 24 15 0.0003002
GO:0048583 regulation of response to stimulus 2704 609 0.0003713
GO:0070663 regulation of leukocyte proliferation 151 53 0.0003905
GO:0098542 defense response to other organism 271 82 0.0004555
GO:0050854 regulation of antigen receptor-mediated signaling pathway 34 19 0.0005325
GO:0050670 regulation of lymphocyte proliferation 146 51 0.0006596
GO:0050771 negative regulation of axonogenesis 40 21 0.0006596
GO:0002275 myeloid cell activation involved in immune response 54 25 0.0007690
GO:0009607 response to biotic stimulus 566 150 0.0007851
GO:0032944 regulation of mononuclear cell proliferation 147 51 0.0007943
GO:0007166 cell surface receptor signaling pathway 2374 538 0.0008028
GO:0007155 cell adhesion 912 230 0.0009323
GO:0022610 biological adhesion 916 231 0.0009343
GO:0007409 axonogenesis 469 130 0.0012616
GO:0002263 cell activation involved in immune response 141 49 0.0012616
GO:0002366 leukocyte activation involved in immune response 141 49 0.0012616
GO:0002683 negative regulation of immune system process 198 64 0.0013289
GO:0009605 response to external stimulus 1589 370 0.0015277
GO:0050857 positive regulation of antigen receptor-mediated signaling pathway 13 10 0.0020446
GO:0061564 axon development 487 133 0.0021299
GO:0045089 positive regulation of innate immune response 196 63 0.0021737
GO:0050817 coagulation 483 131 0.0021737
GO:0051716 cellular response to stimulus 4976 1055 0.0023776
GO:0044707 single-multicellular organism process 4822 1024 0.0023776
GO:0006873 cellular ion homeostasis 365 102 0.0024202
GO:0042060 wound healing 595 156 0.0025298
GO:0007599 hemostasis 485 131 0.0025298
GO:0001816 cytokine production 471 126 0.0026432
GO:0050777 negative regulation of immune response 60 26 0.0027179
GO:0002707 negative regulation of lymphocyte mediated immunity 16 11 0.0031172
GO:0050864 regulation of B cell activation 82 32 0.0031214
GO:0097529 myeloid leukocyte migration 104 37 0.0032928
GO:0035987 endodermal cell differentiation 38 19 0.0033037
GO:0002703 regulation of leukocyte mediated immunity 109 39 0.0035222
GO:0007596 blood coagulation 480 129 0.0035792
GO:0016337 single organismal cell-cell adhesion 283 83 0.0037571
GO:0016477 cell migration 887 218 0.0041712
GO:0042102 positive regulation of T cell proliferation 70 28 0.0042419
GO:0055065 metal ion homeostasis 388 106 0.0044088
GO:0030003 cellular cation homeostasis 358 99 0.0044088
GO:0032501 multicellular organismal process 4965 1048 0.0044502
GO:0030098 lymphocyte differentiation 235 71 0.0045299
GO:0015671 oxygen transport 11 8 0.0050230
GO:0050663 cytokine secretion 108 38 0.0051395
GO:0007411 axon guidance 325 93 0.0051735
GO:0097485 neuron projection guidance 325 93 0.0051735
GO:0042129 regulation of T cell proliferation 108 38 0.0053004
GO:0030217 T cell differentiation 167 54 0.0053004
GO:0002218 activation of innate immune response 167 54 0.0056773
GO:0042100 B cell proliferation 57 24 0.0058838
GO:0072507 divalent inorganic cation homeostasis 275 79 0.0059995
GO:0048667 cell morphogenesis involved in neuron differentiation 535 141 0.0060495
GO:0097530 granulocyte migration 71 27 0.0063491
GO:0048812 neuron projection morphogenesis 544 143 0.0063491
GO:0055080 cation homeostasis 423 113 0.0064103
GO:0002758 innate immune response-activating signal transduction 160 52 0.0064450
GO:0050801 ion homeostasis 476 125 0.0064475
GO:0055082 cellular chemical homeostasis 433 115 0.0064714
GO:0006875 cellular metal ion homeostasis 333 92 0.0071701
GO:0072678 T cell migration 30 15 0.0071701
GO:1901623 regulation of lymphocyte chemotaxis 13 9 0.0074940
GO:0002443 leukocyte mediated immunity 211 63 0.0076032
GO:0050688 regulation of defense response to virus 71 28 0.0076032
GO:0045055 regulated secretory pathway 55 23 0.0089996
GO:0042221 response to chemical 2788 607 0.0100647
GO:0050920 regulation of chemotaxis 108 37 0.0102923
GO:0072503 cellular divalent inorganic cation homeostasis 259 74 0.0105164
GO:0070271 protein complex biogenesis 934 224 0.0107295
GO:0045785 positive regulation of cell adhesion 149 48 0.0108067
GO:0070665 positive regulation of leukocyte proliferation 100 35 0.0109274
GO:0019725 cellular homeostasis 537 137 0.0110723
GO:2000401 regulation of lymphocyte migration 28 14 0.0113290
GO:0050707 regulation of cytokine secretion 90 32 0.0121403
GO:0002700 regulation of production of molecular mediator of immune response 64 25 0.0121403
GO:0048870 cell motility 948 227 0.0121403
GO:0051674 localization of cell 948 227 0.0121403
GO:0006461 protein complex assembly 932 223 0.0121403
GO:0070098 chemokine-mediated signaling pathway 37 17 0.0122788
GO:0006779 porphyrin-containing compound biosynthetic process 27 14 0.0130243
GO:0070664 negative regulation of leukocyte proliferation 50 21 0.0135294
GO:0050856 regulation of T cell receptor signaling pathway 24 13 0.0144383
GO:0010818 T cell chemotaxis 14 9 0.0145773
GO:0001706 endoderm formation 46 20 0.0147199
GO:0002221 pattern recognition receptor signaling pathway 158 50 0.0149617
GO:0032945 negative regulation of mononuclear cell proliferation 47 20 0.0149617
GO:0050672 negative regulation of lymphocyte proliferation 47 20 0.0149617
GO:0001774 microglial cell activation 11 8 0.0154556
GO:2000403 positive regulation of lymphocyte migration 20 11 0.0157627
GO:0007159 leukocyte cell-cell adhesion 44 19 0.0159292
GO:0009306 protein secretion 183 55 0.0159292
GO:0001817 regulation of cytokine production 417 109 0.0165306
GO:0055074 calcium ion homeostasis 255 72 0.0168468
GO:0002440 production of molecular mediator of immune response 103 35 0.0176794
GO:0043900 regulation of multi-organism process 273 76 0.0179757
GO:1990266 neutrophil migration 57 22 0.0181793
GO:0009617 response to bacterium 298 81 0.0184773
GO:0006950 response to stress 2909 627 0.0184773
GO:0031349 positive regulation of defense response 259 73 0.0191981
GO:0031347 regulation of defense response 462 119 0.0204613
GO:0098602 single organism cell adhesion 327 89 0.0228194
GO:0016310 phosphorylation 1655 374 0.0234398
GO:0050671 positive regulation of lymphocyte proliferation 97 33 0.0241728
GO:0050862 positive regulation of T cell receptor signaling pathway 7 6 0.0241728
GO:0015669 gas transport 13 8 0.0241728
GO:0006119 oxidative phosphorylation 70 25 0.0249687
GO:0060099 regulation of phagocytosis, engulfment 7 6 0.0252022
GO:0043244 regulation of protein complex disassembly 77 28 0.0253227
GO:0002282 microglial cell activation involved in immune response 7 6 0.0258671
GO:0065008 regulation of biological quality 2575 559 0.0260490
GO:0006091 generation of precursor metabolites and energy 394 102 0.0262575
GO:0007492 endoderm development 62 24 0.0265989
GO:0016045 detection of bacterium 12 8 0.0265989
GO:0051239 regulation of multicellular organismal process 1819 405 0.0266978
GO:0002820 negative regulation of adaptive immune response 17 10 0.0272645
GO:0050708 regulation of protein secretion 134 42 0.0278188
GO:0071621 granulocyte chemotaxis 67 24 0.0278188
GO:0032946 positive regulation of mononuclear cell proliferation 98 33 0.0278188
GO:0032535 regulation of cellular component size 207 60 0.0279024
GO:0042116 macrophage activation 39 17 0.0299074
GO:0021854 hypothalamus development 12 8 0.0304742
GO:0034109 homotypic cell-cell adhesion 68 25 0.0304742
GO:0006874 cellular calcium ion homeostasis 244 68 0.0311192
GO:0002407 dendritic cell chemotaxis 18 10 0.0316404
GO:1902533 positive regulation of intracellular signal transduction 627 154 0.0316404
GO:0043299 leukocyte degranulation 43 18 0.0316404
GO:0070486 leukocyte aggregation 10 7 0.0316404
GO:0030593 neutrophil chemotaxis 56 21 0.0325268
GO:0050871 positive regulation of B cell activation 50 20 0.0325268
GO:0052564 response to immune response of other organism involved in symbiotic interaction 12 8 0.0325289
GO:0052572 response to host immune response 12 8 0.0325289
GO:0050855 regulation of B cell receptor signaling pathway 12 8 0.0333708
GO:0009611 response to wounding 833 198 0.0342803
GO:2000106 regulation of leukocyte apoptotic process 65 24 0.0346101
GO:0031175 neuron projection development 703 172 0.0346101
GO:0000904 cell morphogenesis involved in differentiation 701 171 0.0373670
GO:0033014 tetrapyrrole biosynthetic process 30 14 0.0386747
GO:0006783 heme biosynthetic process 21 11 0.0401123
GO:0002718 regulation of cytokine production involved in immune response 41 17 0.0410754
GO:0002710 negative regulation of T cell mediated immunity 10 7 0.0410754
GO:0042773 ATP synthesis coupled electron transport 54 20 0.0410754
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 20 0.0410754
GO:0051607 defense response to virus 173 51 0.0416286
GO:0032609 interferon-gamma production 78 27 0.0419610
GO:0002698 negative regulation of immune effector process 61 23 0.0427690
GO:0030155 regulation of cell adhesion 299 81 0.0431876
GO:0090025 regulation of monocyte chemotaxis 13 8 0.0432445
GO:0070228 regulation of lymphocyte apoptotic process 44 18 0.0432445
GO:0071350 cellular response to interleukin-15 10 7 0.0460321
GO:0031663 lipopolysaccharide-mediated signaling pathway 45 18 0.0462290
GO:0030517 negative regulation of axon extension 18 10 0.0462290
GO:0048518 positive regulation of biological process 3684 777 0.0466495
GO:0010819 regulation of T cell chemotaxis 8 6 0.0466495
GO:0010820 positive regulation of T cell chemotaxis 8 6 0.0466495
GO:0036230 granulocyte activation 25 12 0.0475905
GO:0098543 detection of other organism 13 8 0.0477607
GO:0042742 defense response to bacterium 102 32 0.0482518
GO:0050770 regulation of axonogenesis 99 33 0.0495700

Under enriched (62)

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
10394 GO:0010467 gene expression 4322 658 0.0000000
10529 GO:0016070 RNA metabolic process 3693 535 0.0000000
11942 GO:0090304 nucleic acid metabolic process 4166 618 0.0000000
12284 GO:0016071 mRNA metabolic process 615 51 0.0000000
12285 GO:0006139 nucleobase-containing compound metabolic process 5435 879 0.0000000
12288 GO:1901360 organic cyclic compound metabolic process 5728 935 0.0000000
12289 GO:0006396 RNA processing 676 61 0.0000000
12293 GO:0046483 heterocycle metabolic process 5565 909 0.0000000
12294 GO:0006725 cellular aromatic compound metabolic process 5569 910 0.0000000
12315 GO:0034641 cellular nitrogen compound metabolic process 5755 954 0.0000000
12399 GO:0032774 RNA biosynthetic process 3063 466 0.0000000
12405 GO:0006807 nitrogen compound metabolic process 6075 1020 0.0000000
12731 GO:0034654 nucleobase-containing compound biosynthetic process 3350 522 0.0000000
8550 GO:0034645 cellular macromolecule biosynthetic process 3920 630 0.0000002
8549 GO:0044260 cellular macromolecule metabolic process 6484 1114 0.0000013
8548 GO:0019438 aromatic compound biosynthetic process 3410 543 0.0000017
8546 GO:1901362 organic cyclic compound biosynthetic process 3503 560 0.0000017
8547 GO:0006351 transcription, DNA-templated 2952 462 0.0000017
8545 GO:0051252 regulation of RNA metabolic process 2966 466 0.0000025
8544 GO:0006355 regulation of transcription, DNA-templated 2851 446 0.0000028
8542 GO:0018130 heterocycle biosynthetic process 3413 546 0.0000029
8541 GO:0044271 cellular nitrogen compound biosynthetic process 3463 555 0.0000029
8540 GO:0009059 macromolecule biosynthetic process 4025 658 0.0000031
8539 GO:0010468 regulation of gene expression 3465 557 0.0000031
8543 GO:0008380 RNA splicing 332 27 0.0000045
8537 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 498 0.0000045
8536 GO:2001141 regulation of RNA biosynthetic process 2888 455 0.0000049
8535 GO:0006397 mRNA processing 404 38 0.0000100
8533 GO:0043170 macromolecule metabolic process 7144 1252 0.0000160
8534 GO:0042254 ribosome biogenesis 167 8 0.0000238
8538 GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 2 0.0000304
8527 GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 607 0.0000690
8528 GO:0022613 ribonucleoprotein complex biogenesis 280 23 0.0000739
8525 GO:0010556 regulation of macromolecule biosynthetic process 3214 524 0.0000859
8532 GO:0072599 establishment of protein localization to endoplasmic reticulum 111 3 0.0001103
8531 GO:0045047 protein targeting to ER 110 3 0.0001302
8520 GO:0044238 primary metabolic process 8725 1570 0.0001359
8521 GO:0031326 regulation of cellular biosynthetic process 3340 549 0.0001364
8530 GO:0006613 cotranslational protein targeting to membrane 109 3 0.0001393
8529 GO:0006364 rRNA processing 117 4 0.0001487
8519 GO:0009889 regulation of biosynthetic process 3367 555 0.0001707
8523 GO:0034470 ncRNA processing 235 18 0.0001707
8526 GO:0006402 mRNA catabolic process 196 13 0.0001749
8517 GO:0051171 regulation of nitrogen compound metabolic process 3754 629 0.0002499
8524 GO:0016072 rRNA metabolic process 122 5 0.0003028
8522 GO:0000956 nuclear-transcribed mRNA catabolic process 184 12 0.0003028
8515 GO:0009058 biosynthetic process 4899 842 0.0003899
8516 GO:0034660 ncRNA metabolic process 325 32 0.0006336
8514 GO:0044249 cellular biosynthetic process 4756 818 0.0006600
8518 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 5 0.0006758
8513 GO:0071704 organic substance metabolic process 8974 1628 0.0006887
8512 GO:1901576 organic substance biosynthetic process 4830 833 0.0008188
8510 GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 220 19 0.0023049
8511 GO:0000398 mRNA splicing, via spliceosome 220 19 0.0023049
8509 GO:0006401 RNA catabolic process 222 19 0.0023263
8508 GO:0000375 RNA splicing, via transesterification reactions 225 20 0.0030910
8507 GO:0006415 translational termination 95 4 0.0073385
8506 GO:0070972 protein localization to endoplasmic reticulum 128 8 0.0090583
8503 GO:0008152 metabolic process 9725 1793 0.0224337
8505 GO:0006414 translational elongation 121 8 0.0239476
8504 GO:0006612 protein targeting to membrane 171 15 0.0342138
8501 GO:0044237 cellular metabolic process 8652 1587 0.0353622

Negative Effect

Over enriched categories (119)

category term numInCat numDEInCat q.value
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 72 0.0000000
GO:0006414 translational elongation 121 77 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 72 0.0000000
GO:0045047 protein targeting to ER 110 72 0.0000000
GO:0006415 translational termination 95 66 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 72 0.0000000
GO:0016070 RNA metabolic process 3693 847 0.0000000
GO:0090304 nucleic acid metabolic process 4166 928 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 73 0.0000000
GO:0006413 translational initiation 167 89 0.0000000
GO:0010467 gene expression 4322 947 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 74 0.0000000
GO:0016071 mRNA metabolic process 615 206 0.0000000
GO:0006612 protein targeting to membrane 171 85 0.0000000
GO:0034645 cellular macromolecule biosynthetic process 3920 856 0.0000000
GO:0019083 viral transcription 158 78 0.0000000
GO:0032774 RNA biosynthetic process 3063 694 0.0000000
GO:0009059 macromolecule biosynthetic process 4025 866 0.0000000
GO:0018130 heterocycle biosynthetic process 3413 752 0.0000000
GO:0019080 viral gene expression 168 79 0.0000000
GO:0006402 mRNA catabolic process 196 88 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 84 0.0000000
GO:0034654 nucleobase-containing compound biosynthetic process 3350 737 0.0000000
GO:1901362 organic cyclic compound biosynthetic process 3503 764 0.0000000
GO:0044260 cellular macromolecule metabolic process 6484 1284 0.0000000
GO:0044271 cellular nitrogen compound biosynthetic process 3463 756 0.0000000
GO:0019438 aromatic compound biosynthetic process 3410 746 0.0000000
GO:0006401 RNA catabolic process 222 94 0.0000000
GO:0022613 ribonucleoprotein complex biogenesis 280 110 0.0000000
GO:0044249 cellular biosynthetic process 4756 983 0.0000000
GO:1901576 organic substance biosynthetic process 4830 995 0.0000000
GO:0009058 biosynthetic process 4899 1005 0.0000000
GO:0044033 multi-organism metabolic process 178 79 0.0000000
GO:0006412 translation 496 159 0.0000000
GO:0043170 macromolecule metabolic process 7144 1380 0.0000000
GO:0006807 nitrogen compound metabolic process 6075 1200 0.0000000
GO:0034641 cellular nitrogen compound metabolic process 5755 1144 0.0000000
GO:0046483 heterocycle metabolic process 5565 1111 0.0000000
GO:0006139 nucleobase-containing compound metabolic process 5435 1086 0.0000000
GO:0043624 cellular protein complex disassembly 174 75 0.0000000
GO:0006396 RNA processing 676 196 0.0000000
GO:1901360 organic cyclic compound metabolic process 5728 1133 0.0000000
GO:0043241 protein complex disassembly 195 80 0.0000000
GO:0042254 ribosome biogenesis 167 72 0.0000000
GO:0006725 cellular aromatic compound metabolic process 5569 1102 0.0000000
GO:0019058 viral life cycle 303 105 0.0000000
GO:0032984 macromolecular complex disassembly 205 80 0.0000000
GO:0090150 establishment of protein localization to membrane 296 103 0.0000000
GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 669 0.0000000
GO:0010556 regulation of macromolecule biosynthetic process 3214 679 0.0000000
GO:0010468 regulation of gene expression 3465 720 0.0000000
GO:0044238 primary metabolic process 8725 1606 0.0000000
GO:0044237 cellular metabolic process 8652 1593 0.0000000
GO:0031326 regulation of cellular biosynthetic process 3340 696 0.0000000
GO:0006351 transcription, DNA-templated 2952 626 0.0000000
GO:0009889 regulation of biosynthetic process 3367 699 0.0000000
GO:0071704 organic substance metabolic process 8974 1640 0.0000000
GO:0072657 protein localization to membrane 371 115 0.0000000
GO:0051252 regulation of RNA metabolic process 2966 622 0.0000000
GO:0016072 rRNA metabolic process 122 52 0.0000000
GO:0006364 rRNA processing 117 50 0.0000000
GO:0006355 regulation of transcription, DNA-templated 2851 596 0.0000000
GO:2001141 regulation of RNA biosynthetic process 2888 601 0.0000000
GO:0008380 RNA splicing 332 102 0.0000000
GO:0008152 metabolic process 9725 1740 0.0000000
GO:0060255 regulation of macromolecule metabolic process 4402 861 0.0000000
GO:1902578 single-organism localization 426 120 0.0000000
GO:1902580 single-organism cellular localization 426 120 0.0000000
GO:0072594 establishment of protein localization to organelle 456 126 0.0000000
GO:0006397 mRNA processing 404 115 0.0000001
GO:0044764 multi-organism cellular process 682 171 0.0000002
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 220 72 0.0000002
GO:0000398 mRNA splicing, via spliceosome 220 72 0.0000002
GO:0016032 viral process 674 169 0.0000002
GO:0000375 RNA splicing, via transesterification reactions 225 73 0.0000002
GO:0022411 cellular component disassembly 412 115 0.0000002
GO:0006605 protein targeting 497 132 0.0000003
GO:0080090 regulation of primary metabolic process 4733 909 0.0000004
GO:0016482 cytoplasmic transport 825 197 0.0000009
GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 720 0.0000016
GO:0031323 regulation of cellular metabolic process 4749 905 0.0000024
GO:0042274 ribosomal small subunit biogenesis 21 15 0.0000026
GO:0034660 ncRNA metabolic process 325 91 0.0000038
GO:0033365 protein localization to organelle 603 149 0.0000048
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 173 0.0000048
GO:0044419 interspecies interaction between organisms 727 173 0.0000048
GO:0044802 single-organism membrane organization 638 156 0.0000049
GO:0051171 regulation of nitrogen compound metabolic process 3754 730 0.0000051
GO:0044265 cellular macromolecule catabolic process 798 186 0.0000155
GO:0022618 ribonucleoprotein complex assembly 135 47 0.0000198
GO:0034470 ncRNA processing 235 69 0.0000202
GO:0061024 membrane organization 778 180 0.0000278
GO:0009057 macromolecule catabolic process 983 220 0.0000336
GO:0071826 ribonucleoprotein complex subunit organization 141 47 0.0000833
GO:0015931 nucleobase-containing compound transport 169 54 0.0001252
GO:0019222 regulation of metabolic process 5252 976 0.0001548
GO:0006417 regulation of translation 249 71 0.0001880
GO:0050657 nucleic acid transport 144 47 0.0003498
GO:0050658 RNA transport 144 47 0.0003498
GO:0051236 establishment of RNA localization 144 47 0.0003498
GO:0006886 intracellular protein transport 758 172 0.0004427
GO:0006403 RNA localization 151 48 0.0006037
GO:0051028 mRNA transport 124 41 0.0010883
GO:0046907 intracellular transport 1406 289 0.0026581
GO:0001731 formation of translation preinitiation complex 18 11 0.0028007
GO:0030490 maturation of SSU-rRNA 11 8 0.0059045
GO:0071702 organic substance transport 1993 391 0.0071960
GO:0033036 macromolecule localization 2032 399 0.0074144
GO:0000028 ribosomal small subunit assembly 7 6 0.0103476
GO:0070727 cellular macromolecule localization 1129 233 0.0147950
GO:0006405 RNA export from nucleus 80 27 0.0184710
GO:0010746 regulation of plasma membrane long-chain fatty acid transport 5 5 0.0200826
GO:0034613 cellular protein localization 1124 231 0.0200826
GO:1902582 single-organism intracellular transport 1181 240 0.0236196
GO:0042273 ribosomal large subunit biogenesis 16 9 0.0237761
GO:0043933 macromolecular complex subunit organization 1450 288 0.0286846
GO:0010605 negative regulation of macromolecule metabolic process 1458 290 0.0344425
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) 8 6 0.0353112
GO:0000245 spliceosomal complex assembly 44 17 0.0398420

Under enriched (107)

category term numInCat numDEInCat q.value2
7439 GO:0002376 immune system process 1936 227 0.0000009
7438 GO:0007154 cell communication 4559 632 0.0000009
7436 GO:0023052 signaling 4496 623 0.0000009
7437 GO:0044700 single organism signaling 4496 623 0.0000009
7435 GO:0007165 signal transduction 4077 557 0.0000009
7434 GO:0050896 response to stimulus 6126 887 0.0000073
7433 GO:0007166 cell surface receptor signaling pathway 2374 303 0.0000144
7432 GO:0040011 locomotion 1247 141 0.0000240
7431 GO:0016477 cell migration 887 93 0.0000761
7430 GO:0006928 cellular component movement 1405 167 0.0000761
7429 GO:0006955 immune response 1137 125 0.0000761
7427 GO:0048870 cell motility 948 102 0.0000761
7428 GO:0051674 localization of cell 948 102 0.0000761
7426 GO:0009605 response to external stimulus 1589 192 0.0000972
7424 GO:0051716 cellular response to stimulus 4976 719 0.0001772
7425 GO:0042060 wound healing 595 57 0.0001772
7422 GO:0002682 regulation of immune system process 997 111 0.0004809
7423 GO:0016337 single organismal cell-cell adhesion 283 20 0.0006957
7421 GO:0001525 angiogenesis 350 28 0.0009444
7420 GO:0006952 defense response 1178 137 0.0009444
7415 GO:0044707 single-multicellular organism process 4822 704 0.0010974
7419 GO:0001775 cell activation 767 82 0.0010974
7417 GO:0048583 regulation of response to stimulus 2704 371 0.0010974
7414 GO:0032501 multicellular organismal process 4965 727 0.0010974
7418 GO:0001944 vasculature development 509 49 0.0013121
7413 GO:0009611 response to wounding 833 93 0.0015547
7416 GO:0048514 blood vessel morphogenesis 421 38 0.0015552
7411 GO:0048869 cellular developmental process 2893 405 0.0022452
7412 GO:0045321 leukocyte activation 561 56 0.0027693
7406 GO:0044763 single-organism cellular process 9511 1484 0.0027693
7410 GO:0001568 blood vessel development 480 47 0.0032387
7409 GO:0050776 regulation of immune response 666 71 0.0032896
7407 GO:0098602 single organism cell adhesion 327 28 0.0043782
7408 GO:0050900 leukocyte migration 271 20 0.0045724
7403 GO:0009653 anatomical structure morphogenesis 2005 273 0.0052731
7405 GO:0007599 hemostasis 485 49 0.0056811
7402 GO:0022610 biological adhesion 916 110 0.0058583
7396 GO:0030154 cell differentiation 2703 380 0.0060656
7404 GO:0050817 coagulation 483 49 0.0060656
7400 GO:0048646 anatomical structure formation involved in morphogenesis 855 101 0.0060656
7398 GO:0009117 nucleotide metabolic process 1456 189 0.0060906
7395 GO:0006753 nucleoside phosphate metabolic process 1461 190 0.0065053
7397 GO:0007155 cell adhesion 912 110 0.0065053
7399 GO:0007596 blood coagulation 480 49 0.0068917
7389 GO:0055086 nucleobase-containing small molecule metabolic process 1507 198 0.0092457
7394 GO:0042110 T cell activation 347 31 0.0093652
7392 GO:0007186 G-protein coupled receptor signaling pathway 549 57 0.0094358
7391 GO:0050878 regulation of body fluid levels 579 63 0.0094358
7387 GO:0006163 purine nucleotide metabolic process 1313 170 0.0104238
7386 GO:0009116 nucleoside metabolic process 1238 159 0.0107174
7385 GO:1901657 glycosyl compound metabolic process 1252 161 0.0107174
7388 GO:0001503 ossification 315 28 0.0129363
7381 GO:0009150 purine ribonucleotide metabolic process 1292 168 0.0136640
7380 GO:0019693 ribose phosphate metabolic process 1311 171 0.0143968
7379 GO:0007267 cell-cell signaling 915 111 0.0151974
7376 GO:0009259 ribonucleotide metabolic process 1307 171 0.0167010
7368 GO:0044767 single-organism developmental process 4247 631 0.0172923
7374 GO:0009119 ribonucleoside metabolic process 1218 158 0.0172923
7372 GO:0072521 purine-containing compound metabolic process 1346 177 0.0172923
7369 GO:0010646 regulation of cell communication 2327 328 0.0172923
7365 GO:0044699 single-organism process 10471 1658 0.0172923
7377 GO:0006935 chemotaxis 558 61 0.0173497
7378 GO:0042330 taxis 558 61 0.0173497
7363 GO:0035556 intracellular signal transduction 1995 276 0.0186663
7362 GO:0009966 regulation of signal transduction 2098 293 0.0186663
7375 GO:0046649 lymphocyte activation 480 50 0.0189851
7370 GO:0007268 synaptic transmission 566 64 0.0189851
7359 GO:0048856 anatomical structure development 3825 565 0.0189851
7360 GO:0050793 regulation of developmental process 1512 202 0.0189851
7367 GO:0045087 innate immune response 724 84 0.0189851
7390 GO:0007187 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger 100 4 0.0198562
7371 GO:0050865 regulation of cell activation 366 35 0.0205594
7358 GO:0046128 purine ribonucleoside metabolic process 1195 156 0.0216610
7354 GO:0065008 regulation of biological quality 2575 366 0.0235769
7356 GO:0044093 positive regulation of molecular function 1425 191 0.0241232
7352 GO:1901135 carbohydrate derivative metabolic process 1917 266 0.0242664
7355 GO:0042278 purine nucleoside metabolic process 1198 157 0.0247171
7353 GO:2000026 regulation of multicellular organismal development 1140 147 0.0248445
7350 GO:0006950 response to stress 2909 416 0.0248445
7401 GO:0050868 negative regulation of T cell activation 64 1 0.0249854
7349 GO:0009205 purine ribonucleoside triphosphate metabolic process 1126 147 0.0280151
7366 GO:0045165 cell fate commitment 172 12 0.0282675
7347 GO:0051336 regulation of hydrolase activity 1039 134 0.0282675
7345 GO:0009144 purine nucleoside triphosphate metabolic process 1132 148 0.0282675
7384 GO:0015698 inorganic anion transport 83 3 0.0285372
7382 GO:0051250 negative regulation of lymphocyte activation 86 3 0.0295018
7339 GO:0032502 developmental process 4292 643 0.0295018
7364 GO:0030278 regulation of ossification 152 10 0.0298640
7342 GO:0009141 nucleoside triphosphate metabolic process 1150 151 0.0298717
7341 GO:0043085 positive regulation of catalytic activity 1225 162 0.0298717
7337 GO:0023051 regulation of signaling 2321 331 0.0311025
7393 GO:1902476 chloride transmembrane transport 59 1 0.0315110
7338 GO:0030030 cell projection organization 991 129 0.0334459
7331 GO:0048731 system development 3248 477 0.0338099
7335 GO:0009199 ribonucleoside triphosphate metabolic process 1132 149 0.0338099
7383 GO:0098661 inorganic anion transmembrane transport 70 2 0.0338099
9667 GO:0032945 negative regulation of mononuclear cell proliferation 47 0 0.0338099
10163 GO:0050672 negative regulation of lymphocyte proliferation 47 0 0.0338099
7333 GO:0051239 regulation of multicellular organismal process 1819 251 0.0338099
7334 GO:0051345 positive regulation of hydrolase activity 763 95 0.0360043
7343 GO:0002694 regulation of leukocyte activation 340 33 0.0362163
7344 GO:0048705 skeletal system morphogenesis 183 14 0.0421566
7332 GO:0007264 small GTPase mediated signal transduction 486 55 0.0421704
7328 GO:0043207 response to external biotic stimulus 535 59 0.0447747
7329 GO:0051707 response to other organism 535 59 0.0447747
7357 GO:0002695 negative regulation of leukocyte activation 102 5 0.0462784
7327 GO:0002521 leukocyte differentiation 353 36 0.0496859

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)