This report has goseq results for fasting 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_all_genes.txt"
outFile <- "pept"

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 3984 DE genes with postive effect and 3516 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 (120)

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:0006413 translational initiation 167 120 0.0000000
GO:0006415 translational termination 95 78 0.0000000
GO:0006414 translational elongation 121 93 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 91 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 84 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 85 0.0000000
GO:0045047 protein targeting to ER 110 85 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 85 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 94 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 121 0.0000000
GO:0006402 mRNA catabolic process 196 126 0.0000000
GO:0019083 viral transcription 158 105 0.0000000
GO:0006401 RNA catabolic process 222 138 0.0000000
GO:0006955 immune response 1137 551 0.0000000
GO:0006612 protein targeting to membrane 171 111 0.0000000
GO:0019080 viral gene expression 168 107 0.0000000
GO:0044033 multi-organism metabolic process 178 112 0.0000000
GO:0043241 protein complex disassembly 195 119 0.0000000
GO:0043933 macromolecular complex subunit organization 1450 673 0.0000001
GO:0043624 cellular protein complex disassembly 174 108 0.0000001
GO:0071822 protein complex subunit organization 1283 601 0.0000001
GO:0002757 immune response-activating signal transduction 333 185 0.0000002
GO:0045321 leukocyte activation 561 287 0.0000002
GO:0046649 lymphocyte activation 480 250 0.0000003
GO:0032984 macromolecular complex disassembly 205 121 0.0000004
GO:0006412 translation 496 254 0.0000006
GO:0002376 immune system process 1936 865 0.0000008
GO:0002684 positive regulation of immune system process 610 303 0.0000023
GO:0050776 regulation of immune response 666 328 0.0000025
GO:0002253 activation of immune response 373 198 0.0000031
GO:0002764 immune response-regulating signaling pathway 428 223 0.0000041
GO:0050778 positive regulation of immune response 441 227 0.0000051
GO:0002682 regulation of immune system process 997 467 0.0000055
GO:0044802 single-organism membrane organization 638 311 0.0000153
GO:0090150 establishment of protein localization to membrane 296 158 0.0000181
GO:0072657 protein localization to membrane 371 192 0.0000203
GO:0045087 innate immune response 724 346 0.0000262
GO:0019058 viral life cycle 303 159 0.0000453
GO:1902578 single-organism localization 426 215 0.0000474
GO:1902580 single-organism cellular localization 426 215 0.0000474
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 115 0.0000535
GO:0016482 cytoplasmic transport 825 388 0.0000541
GO:0001775 cell activation 767 362 0.0000628
GO:0061024 membrane organization 778 367 0.0000654
GO:0042110 T cell activation 347 179 0.0000714
GO:0006968 cellular defense response 45 34 0.0000818
GO:0022411 cellular component disassembly 412 208 0.0000854
GO:0051249 regulation of lymphocyte activation 298 156 0.0000933
GO:0051251 positive regulation of lymphocyte activation 212 116 0.0001475
GO:0050851 antigen receptor-mediated signaling pathway 138 82 0.0002228
GO:0050867 positive regulation of cell activation 239 127 0.0002975
GO:0031294 lymphocyte costimulation 63 43 0.0003077
GO:0031295 T cell costimulation 63 43 0.0003077
GO:0002694 regulation of leukocyte activation 340 173 0.0003388
GO:0033036 macromolecule localization 2032 887 0.0003388
GO:0002696 positive regulation of leukocyte activation 230 123 0.0003955
GO:0046651 lymphocyte proliferation 189 104 0.0005551
GO:0006952 defense response 1178 527 0.0006566
GO:0002252 immune effector process 504 243 0.0007594
GO:1902582 single-organism intracellular transport 1181 531 0.0009932
GO:0032943 mononuclear cell proliferation 191 104 0.0010051
GO:0072594 establishment of protein localization to organelle 456 222 0.0010706
GO:0042113 B cell activation 169 94 0.0013387
GO:0070661 leukocyte proliferation 200 107 0.0018081
GO:0002274 myeloid leukocyte activation 123 71 0.0020940
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 159 0.0022024
GO:0050865 regulation of cell activation 366 181 0.0022977
GO:0033365 protein localization to organelle 603 284 0.0025305
GO:0044764 multi-organism cellular process 682 317 0.0026647
GO:0006417 regulation of translation 249 130 0.0026845
GO:0044267 cellular protein metabolic process 3491 1469 0.0028992
GO:0050863 regulation of T cell activation 226 118 0.0029747
GO:0065003 macromolecular complex assembly 1091 489 0.0030019
GO:0016032 viral process 674 313 0.0030019
GO:0098542 defense response to other organism 271 137 0.0033887
GO:0002831 regulation of response to biotic stimulus 97 58 0.0038091
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 334 0.0042007
GO:0044419 interspecies interaction between organisms 727 334 0.0042007
GO:0045088 regulation of innate immune response 243 126 0.0045603
GO:0019538 protein metabolic process 4128 1717 0.0049752
GO:0050870 positive regulation of T cell activation 165 89 0.0057435
GO:0008104 protein localization 1760 763 0.0059402
GO:0051641 cellular localization 2267 968 0.0068901
GO:0042100 B cell proliferation 57 37 0.0069041
GO:0070663 regulation of leukocyte proliferation 151 82 0.0069854
GO:0006605 protein targeting 497 235 0.0076213
GO:0070727 cellular macromolecule localization 1129 501 0.0102997
GO:0050670 regulation of lymphocyte proliferation 146 79 0.0106192
GO:0002407 dendritic cell chemotaxis 18 15 0.0133197
GO:0031663 lipopolysaccharide-mediated signaling pathway 45 30 0.0136533
GO:0032944 regulation of mononuclear cell proliferation 147 79 0.0140794
GO:0043207 response to external biotic stimulus 535 247 0.0152519
GO:0051707 response to other organism 535 247 0.0152519
GO:0034613 cellular protein localization 1124 497 0.0154437
GO:0009607 response to biotic stimulus 566 260 0.0154437
GO:0070271 protein complex biogenesis 934 417 0.0155427
GO:0002758 innate immune response-activating signal transduction 160 86 0.0155552
GO:0002218 activation of innate immune response 167 89 0.0170259
GO:0045089 positive regulation of innate immune response 196 102 0.0173908
GO:0050853 B cell receptor signaling pathway 39 27 0.0173908
GO:0042098 T cell proliferation 135 73 0.0180567
GO:0046907 intracellular transport 1406 611 0.0200056
GO:0006461 protein complex assembly 932 415 0.0200056
GO:0050852 T cell receptor signaling pathway 106 60 0.0216003
GO:0036336 dendritic cell migration 22 17 0.0247675
GO:0002224 toll-like receptor signaling pathway 136 74 0.0256751
GO:0030217 T cell differentiation 167 88 0.0271389
GO:0002221 pattern recognition receptor signaling pathway 158 84 0.0271389
GO:0002443 leukocyte mediated immunity 211 106 0.0279394
GO:0030595 leukocyte chemotaxis 130 69 0.0287355
GO:0022613 ribonucleoprotein complex biogenesis 280 137 0.0315374
GO:0030098 lymphocyte differentiation 235 118 0.0320441
GO:0016071 mRNA metabolic process 615 280 0.0322517
GO:0002697 regulation of immune effector process 231 115 0.0364940
GO:0051246 regulation of protein metabolic process 1748 746 0.0450712
GO:0048584 positive regulation of response to stimulus 1324 572 0.0466155
GO:0030889 negative regulation of B cell proliferation 14 12 0.0466155
GO:0042102 positive regulation of T cell proliferation 70 41 0.0466155
GO:0050864 regulation of B cell activation 82 47 0.0466629
GO:0071216 cellular response to biotic stimulus 125 67 0.0485477

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
10312 GO:0007588 excretion 42 5 1
10311 GO:0048663 neuron fate commitment 38 5 1
11873 GO:0060850 regulation of transcription involved in cell fate commitment 15 0 1
10310 GO:0051148 negative regulation of muscle cell differentiation 35 5 1
10305 GO:0050679 positive regulation of epithelial cell proliferation 123 32 1
10296 GO:0061448 connective tissue development 186 54 1
10291 GO:0030030 cell projection organization 991 349 1
10306 GO:0007431 salivary gland development 36 6 1
10293 GO:0045165 cell fate commitment 172 49 1
10303 GO:0002088 lens development in camera-type eye 53 11 1
10285 GO:0000904 cell morphogenesis involved in differentiation 701 242 1
10301 GO:0019935 cyclic-nucleotide-mediated signaling 43 8 1
10309 GO:0070306 lens fiber cell differentiation 20 2 1
11792 GO:0060395 SMAD protein signal transduction 11 0 1
12053 GO:0071467 cellular response to pH 11 0 1
10290 GO:0007224 smoothened signaling pathway 105 28 1
10308 GO:0042133 neurotransmitter metabolic process 20 2 1
10295 GO:0048708 astrocyte differentiation 42 8 1
10275 GO:0009887 organ morphogenesis 691 238 1
10298 GO:0035924 cellular response to vascular endothelial growth factor stimulus 31 5 1

Positive Effect

Over enriched categories (235)

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 405 0.0000000
GO:0002376 immune system process 1936 613 0.0000000
GO:0045321 leukocyte activation 561 224 0.0000000
GO:0001775 cell activation 767 276 0.0000000
GO:0046649 lymphocyte activation 480 192 0.0000000
GO:0050776 regulation of immune response 666 245 0.0000000
GO:0002682 regulation of immune system process 997 336 0.0000000
GO:0002684 positive regulation of immune system process 610 224 0.0000000
GO:0006952 defense response 1178 374 0.0000000
GO:0002757 immune response-activating signal transduction 333 141 0.0000000
GO:0050778 positive regulation of immune response 441 171 0.0000000
GO:0045087 innate immune response 724 250 0.0000000
GO:0042110 T cell activation 347 142 0.0000000
GO:0002253 activation of immune response 373 148 0.0000000
GO:0002764 immune response-regulating signaling pathway 428 161 0.0000000
GO:0002252 immune effector process 504 180 0.0000000
GO:0002694 regulation of leukocyte activation 340 132 0.0000000
GO:0051249 regulation of lymphocyte activation 298 119 0.0000000
GO:0050896 response to stimulus 6126 1512 0.0000000
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 89 0.0000000
GO:0050865 regulation of cell activation 366 137 0.0000000
GO:0009607 response to biotic stimulus 566 190 0.0000000
GO:0046651 lymphocyte proliferation 189 82 0.0000000
GO:0043207 response to external biotic stimulus 535 181 0.0000000
GO:0051707 response to other organism 535 181 0.0000000
GO:0050851 antigen receptor-mediated signaling pathway 138 66 0.0000000
GO:0002274 myeloid leukocyte activation 123 60 0.0000000
GO:0050863 regulation of T cell activation 226 93 0.0000000
GO:0002696 positive regulation of leukocyte activation 230 94 0.0000000
GO:0032943 mononuclear cell proliferation 191 82 0.0000000
GO:0051251 positive regulation of lymphocyte activation 212 88 0.0000000
GO:0050867 positive regulation of cell activation 239 96 0.0000000
GO:0050900 leukocyte migration 271 105 0.0000000
GO:0070661 leukocyte proliferation 200 84 0.0000000
GO:0098542 defense response to other organism 271 104 0.0000000
GO:0006950 response to stress 2909 760 0.0000001
GO:0050870 positive regulation of T cell activation 165 71 0.0000002
GO:0006968 cellular defense response 45 29 0.0000002
GO:0042098 T cell proliferation 135 61 0.0000003
GO:0001816 cytokine production 471 157 0.0000003
GO:0007165 signal transduction 4077 1028 0.0000004
GO:0023052 signaling 4496 1123 0.0000005
GO:0044700 single organism signaling 4496 1123 0.0000005
GO:0007154 cell communication 4559 1137 0.0000005
GO:0002443 leukocyte mediated immunity 211 83 0.0000005
GO:0044763 single-organism cellular process 9511 2226 0.0000005
GO:0045088 regulation of innate immune response 243 94 0.0000005
GO:0042113 B cell activation 169 71 0.0000009
GO:0031294 lymphocyte costimulation 63 35 0.0000009
GO:0031295 T cell costimulation 63 35 0.0000009
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 113 0.0000009
GO:0048518 positive regulation of biological process 3684 930 0.0000013
GO:0048583 regulation of response to stimulus 2704 704 0.0000014
GO:0070663 regulation of leukocyte proliferation 151 64 0.0000017
GO:0048584 positive regulation of response to stimulus 1324 371 0.0000020
GO:0050670 regulation of lymphocyte proliferation 146 62 0.0000026
GO:0032944 regulation of mononuclear cell proliferation 147 62 0.0000035
GO:0002263 cell activation involved in immune response 141 60 0.0000048
GO:0002366 leukocyte activation involved in immune response 141 60 0.0000048
GO:0042129 regulation of T cell proliferation 108 49 0.0000056
GO:0001817 regulation of cytokine production 417 137 0.0000062
GO:0002697 regulation of immune effector process 231 86 0.0000066
GO:0030595 leukocyte chemotaxis 130 55 0.0000066
GO:0072676 lymphocyte migration 47 27 0.0000092
GO:0051716 cellular response to stimulus 4976 1212 0.0000164
GO:0009617 response to bacterium 298 102 0.0000188
GO:0030098 lymphocyte differentiation 235 86 0.0000221
GO:0031347 regulation of defense response 462 147 0.0000238
GO:0050853 B cell receptor signaling pathway 39 24 0.0000245
GO:0002831 regulation of response to biotic stimulus 97 44 0.0000435
GO:0050852 T cell receptor signaling pathway 106 47 0.0000441
GO:0030217 T cell differentiation 167 66 0.0000451
GO:0048522 positive regulation of cellular process 3307 827 0.0000861
GO:0042102 positive regulation of T cell proliferation 70 34 0.0000861
GO:0007599 hemostasis 485 151 0.0001005
GO:0044699 single-organism process 10471 2405 0.0001575
GO:0001819 positive regulation of cytokine production 245 85 0.0001575
GO:0045089 positive regulation of innate immune response 196 73 0.0001575
GO:0002275 myeloid cell activation involved in immune response 54 28 0.0001592
GO:0050817 coagulation 483 150 0.0001931
GO:0002250 adaptive immune response 194 71 0.0001960
GO:0060326 cell chemotaxis 177 65 0.0001960
GO:0070271 protein complex biogenesis 934 263 0.0002009
GO:0007596 blood coagulation 480 149 0.0002029
GO:0009605 response to external stimulus 1589 421 0.0002029
GO:0002521 leukocyte differentiation 353 115 0.0002116
GO:0022904 respiratory electron transport chain 105 43 0.0002296
GO:0050777 negative regulation of immune response 60 30 0.0002780
GO:0042742 defense response to bacterium 102 42 0.0002828
GO:0022900 electron transport chain 106 43 0.0003071
GO:0006461 protein complex assembly 932 261 0.0003179
GO:0070098 chemokine-mediated signaling pathway 37 21 0.0003655
GO:0031349 positive regulation of defense response 259 88 0.0003892
GO:0002703 regulation of leukocyte mediated immunity 109 45 0.0003946
GO:0002218 activation of innate immune response 167 63 0.0004517
GO:0006954 inflammatory response 473 143 0.0005326
GO:0007166 cell surface receptor signaling pathway 2374 606 0.0005326
GO:0009620 response to fungus 23 15 0.0005648
GO:0042100 B cell proliferation 57 28 0.0005800
GO:0043299 leukocyte degranulation 43 23 0.0006285
GO:0002683 negative regulation of immune system process 198 71 0.0006664
GO:1990266 neutrophil migration 57 27 0.0007574
GO:0050864 regulation of B cell activation 82 36 0.0008089
GO:0002758 innate immune response-activating signal transduction 160 60 0.0008960
GO:0048247 lymphocyte chemotaxis 24 15 0.0010395
GO:0097530 granulocyte migration 71 31 0.0011616
GO:0070665 positive regulation of leukocyte proliferation 100 41 0.0011616
GO:0009306 protein secretion 183 65 0.0012390
GO:0042060 wound healing 595 175 0.0012442
GO:0002449 lymphocyte mediated immunity 163 59 0.0013365
GO:0065003 macromolecular complex assembly 1091 296 0.0013850
GO:0042221 response to chemical 2788 695 0.0014101
GO:0002444 myeloid leukocyte mediated immunity 54 26 0.0014326
GO:0030593 neutrophil chemotaxis 56 26 0.0015539
GO:0097529 myeloid leukocyte migration 104 41 0.0015539
GO:0034097 response to cytokine 534 158 0.0016675
GO:0051607 defense response to virus 173 62 0.0017911
GO:0045576 mast cell activation 40 21 0.0017968
GO:0010033 response to organic substance 2043 522 0.0018814
GO:0006119 oxidative phosphorylation 70 30 0.0021475
GO:0002221 pattern recognition receptor signaling pathway 158 58 0.0022626
GO:0042119 neutrophil activation 22 14 0.0022628
GO:0036336 dendritic cell migration 22 14 0.0022628
GO:0019221 cytokine-mediated signaling pathway 345 108 0.0024541
GO:0045055 regulated secretory pathway 55 26 0.0025499
GO:0050671 positive regulation of lymphocyte proliferation 97 39 0.0026750
GO:0043900 regulation of multi-organism process 273 88 0.0028605
GO:0050663 cytokine secretion 108 42 0.0028605
GO:0032615 interleukin-12 production 41 21 0.0028981
GO:0036230 granulocyte activation 25 15 0.0029004
GO:0032945 negative regulation of mononuclear cell proliferation 47 23 0.0031742
GO:0050672 negative regulation of lymphocyte proliferation 47 23 0.0031742
GO:0070664 negative regulation of leukocyte proliferation 50 24 0.0032004
GO:0009615 response to virus 261 85 0.0033225
GO:0032946 positive regulation of mononuclear cell proliferation 98 39 0.0033225
GO:0002407 dendritic cell chemotaxis 18 12 0.0036319
GO:0045333 cellular respiration 158 55 0.0037693
GO:0050688 regulation of defense response to virus 71 31 0.0038569
GO:0002448 mast cell mediated immunity 28 16 0.0039620
GO:0071621 granulocyte chemotaxis 67 28 0.0056522
GO:0002507 tolerance induction 16 11 0.0061820
GO:0032655 regulation of interleukin-12 production 40 20 0.0062534
GO:0032609 interferon-gamma production 78 32 0.0063716
GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 172 59 0.0069099
GO:0002706 regulation of lymphocyte mediated immunity 85 34 0.0078165
GO:0071345 cellular response to cytokine stimulus 452 133 0.0082572
GO:0032729 positive regulation of interferon-gamma production 35 18 0.0088414
GO:0030889 negative regulation of B cell proliferation 14 10 0.0093430
GO:0043303 mast cell degranulation 27 15 0.0097666
GO:0009611 response to wounding 833 227 0.0097676
GO:0015671 oxygen transport 11 8 0.0097676
GO:2000401 regulation of lymphocyte migration 28 15 0.0100647
GO:0050707 regulation of cytokine secretion 90 35 0.0104067
GO:0019882 antigen processing and presentation 215 70 0.0105388
GO:0006935 chemotaxis 558 158 0.0108111
GO:0042330 taxis 558 158 0.0108111
GO:0065008 regulation of biological quality 2575 636 0.0112549
GO:0032496 response to lipopolysaccharide 200 66 0.0112752
GO:0002224 toll-like receptor signaling pathway 136 49 0.0125674
GO:0050832 defense response to fungus 11 8 0.0125674
GO:0051049 regulation of transport 1194 313 0.0125674
GO:0006909 phagocytosis 162 56 0.0125904
GO:0033014 tetrapyrrole biosynthetic process 30 16 0.0131222
GO:0042773 ATP synthesis coupled electron transport 54 23 0.0137157
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 23 0.0137157
GO:0071350 cellular response to interleukin-15 10 8 0.0137248
GO:1902105 regulation of leukocyte differentiation 178 60 0.0137248
GO:0042116 macrophage activation 39 19 0.0148745
GO:0002279 mast cell activation involved in immune response 28 15 0.0151674
GO:0051246 regulation of protein metabolic process 1748 443 0.0152697
GO:0045619 regulation of lymphocyte differentiation 104 39 0.0167747
GO:0002237 response to molecule of bacterial origin 214 69 0.0167747
GO:0050708 regulation of protein secretion 134 47 0.0167747
GO:0045577 regulation of B cell differentiation 20 12 0.0181002
GO:0035556 intracellular signal transduction 1995 501 0.0188338
GO:0008089 anterograde axon cargo transport 23 13 0.0195800
GO:0032940 secretion by cell 682 187 0.0206823
GO:0016310 phosphorylation 1655 421 0.0224190
GO:0032649 regulation of interferon-gamma production 67 27 0.0231259
GO:0072678 T cell migration 30 15 0.0231593
GO:0070887 cellular response to chemical stimulus 1926 481 0.0231593
GO:0002704 negative regulation of leukocyte mediated immunity 18 11 0.0238312
GO:0050854 regulation of antigen receptor-mediated signaling pathway 34 17 0.0242481
GO:0050871 positive regulation of B cell activation 50 22 0.0245082
GO:0007159 leukocyte cell-cell adhesion 44 20 0.0245082
GO:0002517 T cell tolerance induction 11 8 0.0245082
GO:0032268 regulation of cellular protein metabolic process 1414 363 0.0248219
GO:0080134 regulation of response to stress 852 228 0.0250276
GO:0034341 response to interferon-gamma 108 39 0.0253098
GO:0016265 death 1755 441 0.0255471
GO:0048002 antigen processing and presentation of peptide antigen 180 59 0.0260170
GO:0008219 cell death 1751 440 0.0260170
GO:0012501 programmed cell death 1539 390 0.0262155
GO:0070672 response to interleukin-15 13 9 0.0269242
GO:0045579 positive regulation of B cell differentiation 11 8 0.0286561
GO:0001906 cell killing 75 29 0.0295347
GO:0001774 microglial cell activation 11 8 0.0305507
GO:0002699 positive regulation of immune effector process 109 39 0.0305507
GO:0010818 T cell chemotaxis 14 9 0.0305507
GO:0002520 immune system development 648 178 0.0305787
GO:0086091 regulation of heart rate by cardiac conduction 21 12 0.0309182
GO:0050878 regulation of body fluid levels 579 161 0.0309364
GO:0043300 regulation of leukocyte degranulation 24 13 0.0315589
GO:1903305 regulation of regulated secretory pathway 24 13 0.0315589
GO:0002819 regulation of adaptive immune response 99 36 0.0325361
GO:0043623 cellular protein complex assembly 352 103 0.0339053
GO:0032101 regulation of response to external stimulus 501 140 0.0341415
GO:0002707 negative regulation of lymphocyte mediated immunity 16 10 0.0341415
GO:0035987 endodermal cell differentiation 38 18 0.0341415
GO:0032648 regulation of interferon-beta production 35 17 0.0343045
GO:0050764 regulation of phagocytosis 45 20 0.0345578
GO:0006915 apoptotic process 1521 384 0.0356778
GO:0006779 porphyrin-containing compound biosynthetic process 27 14 0.0365336
GO:0002440 production of molecular mediator of immune response 103 37 0.0366457
GO:2000106 regulation of leukocyte apoptotic process 65 26 0.0368517
GO:2000403 positive regulation of lymphocyte migration 20 11 0.0371272
GO:0002695 negative regulation of leukocyte activation 102 37 0.0371272
GO:0033077 T cell differentiation in thymus 67 27 0.0390752
GO:0030097 hemopoiesis 587 162 0.0392723
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 36 0.0409712
GO:0006091 generation of precursor metabolites and energy 394 112 0.0409712
GO:0002698 negative regulation of immune effector process 61 25 0.0420188
GO:0002282 microglial cell activation involved in immune response 7 6 0.0420188
GO:0050830 defense response to Gram-positive bacterium 38 17 0.0429758
GO:0030888 regulation of B cell proliferation 46 20 0.0443266
GO:0002532 production of molecular mediator involved in inflammatory response 25 13 0.0457531
GO:0009215 purine deoxyribonucleoside triphosphate metabolic process 12 8 0.0459019
GO:0051259 protein oligomerization 341 100 0.0459019
GO:0015669 gas transport 13 8 0.0459258
GO:0002283 neutrophil activation involved in immune response 12 8 0.0459258
GO:0071216 cellular response to biotic stimulus 125 43 0.0460369
GO:0006796 phosphate-containing compound metabolic process 3226 779 0.0460369
GO:0051250 negative regulation of lymphocyte activation 86 32 0.0474497
GO:0060307 regulation of ventricular cardiac muscle cell membrane repolarization 12 8 0.0488195
GO:0046631 alpha-beta T cell activation 86 32 0.0494336

Under enriched (31)

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
12463 GO:0016070 RNA metabolic process 3693 672 0.0000000
12692 GO:0090304 nucleic acid metabolic process 4166 774 0.0000000
8965 GO:0032774 RNA biosynthetic process 3063 558 0.0000102
8964 GO:0034654 nucleobase-containing compound biosynthetic process 3350 618 0.0000111
8963 GO:0010467 gene expression 4322 829 0.0000937
8962 GO:1901362 organic cyclic compound biosynthetic process 3503 659 0.0001059
8960 GO:1901360 organic cyclic compound metabolic process 5728 1134 0.0001428
8961 GO:0019438 aromatic compound biosynthetic process 3410 642 0.0001428
8959 GO:0018130 heterocycle biosynthetic process 3413 643 0.0001428
8958 GO:0006139 nucleobase-containing compound metabolic process 5435 1073 0.0001800
8957 GO:0044271 cellular nitrogen compound biosynthetic process 3463 655 0.0001800
8956 GO:0006355 regulation of transcription, DNA-templated 2851 531 0.0002477
8955 GO:0006351 transcription, DNA-templated 2952 553 0.0003220
8954 GO:0006725 cellular aromatic compound metabolic process 5569 1106 0.0003220
8953 GO:0046483 heterocycle metabolic process 5565 1106 0.0003588
8952 GO:2001141 regulation of RNA biosynthetic process 2888 543 0.0006205
8951 GO:0051252 regulation of RNA metabolic process 2966 560 0.0006891
8950 GO:0034641 cellular nitrogen compound metabolic process 5755 1152 0.0008436
8949 GO:0006807 nitrogen compound metabolic process 6075 1225 0.0014252
8948 GO:0034645 cellular macromolecule biosynthetic process 3920 764 0.0018479
8946 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 603 0.0048107
8947 GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 7 0.0148239
8941 GO:0009059 macromolecule biosynthetic process 4025 797 0.0152829
8940 GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 725 0.0202000
8945 GO:0072599 establishment of protein localization to endoplasmic reticulum 111 8 0.0231777
8939 GO:0010468 regulation of gene expression 3465 682 0.0231777
8943 GO:0045047 protein targeting to ER 110 8 0.0263531
8944 GO:0006415 translational termination 95 6 0.0274794
8942 GO:0006613 cotranslational protein targeting to membrane 109 8 0.0281780
8938 GO:0006396 RNA processing 676 110 0.0417109
8937 GO:0031326 regulation of cellular biosynthetic process 3340 660 0.0492148

Negative Effect

Over enriched categories (88)

category term numInCat numDEInCat q.value
GO:0006415 translational termination 95 72 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 77 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 77 0.0000000
GO:0045047 protein targeting to ER 110 77 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 77 0.0000000
GO:0006414 translational elongation 121 79 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 78 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 79 0.0000000
GO:0006413 translational initiation 167 91 0.0000000
GO:0019083 viral transcription 158 84 0.0000000
GO:0006612 protein targeting to membrane 171 87 0.0000000
GO:0019080 viral gene expression 168 84 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 88 0.0000000
GO:0044033 multi-organism metabolic process 178 84 0.0000000
GO:0006402 mRNA catabolic process 196 90 0.0000000
GO:0006401 RNA catabolic process 222 96 0.0000000
GO:0043624 cellular protein complex disassembly 174 81 0.0000000
GO:0043241 protein complex disassembly 195 87 0.0000000
GO:0032984 macromolecular complex disassembly 205 87 0.0000000
GO:0016070 RNA metabolic process 3693 795 0.0000000
GO:0090304 nucleic acid metabolic process 4166 879 0.0000000
GO:0090150 establishment of protein localization to membrane 296 108 0.0000000
GO:0032774 RNA biosynthetic process 3063 671 0.0000000
GO:0019058 viral life cycle 303 104 0.0000000
GO:0034654 nucleobase-containing compound biosynthetic process 3350 714 0.0000000
GO:0018130 heterocycle biosynthetic process 3413 725 0.0000000
GO:0019438 aromatic compound biosynthetic process 3410 722 0.0000000
GO:1901362 organic cyclic compound biosynthetic process 3503 738 0.0000000
GO:0010467 gene expression 4322 885 0.0000000
GO:0044271 cellular nitrogen compound biosynthetic process 3463 729 0.0000000
GO:0016071 mRNA metabolic process 615 173 0.0000000
GO:0072657 protein localization to membrane 371 118 0.0000000
GO:0034645 cellular macromolecule biosynthetic process 3920 809 0.0000000
GO:0006412 translation 496 143 0.0000000
GO:0022411 cellular component disassembly 412 125 0.0000000
GO:0009059 macromolecule biosynthetic process 4025 819 0.0000000
GO:0022613 ribonucleoprotein complex biogenesis 280 91 0.0000000
GO:0044260 cellular macromolecule metabolic process 6484 1242 0.0000000
GO:1902578 single-organism localization 426 123 0.0000000
GO:1902580 single-organism cellular localization 426 123 0.0000000
GO:0042254 ribosome biogenesis 167 61 0.0000000
GO:0072594 establishment of protein localization to organelle 456 129 0.0000000
GO:1901360 organic cyclic compound metabolic process 5728 1112 0.0000001
GO:0006139 nucleobase-containing compound metabolic process 5435 1062 0.0000001
GO:0046483 heterocycle metabolic process 5565 1084 0.0000001
GO:0044249 cellular biosynthetic process 4756 937 0.0000001
GO:0006807 nitrogen compound metabolic process 6075 1170 0.0000001
GO:0009058 biosynthetic process 4899 960 0.0000001
GO:0034641 cellular nitrogen compound metabolic process 5755 1113 0.0000001
GO:0006725 cellular aromatic compound metabolic process 5569 1080 0.0000002
GO:0044802 single-organism membrane organization 638 167 0.0000002
GO:1901576 organic substance biosynthetic process 4830 945 0.0000002
GO:0043170 macromolecule metabolic process 7144 1346 0.0000002
GO:0006605 protein targeting 497 136 0.0000002
GO:0016072 rRNA metabolic process 122 46 0.0000022
GO:0061024 membrane organization 778 190 0.0000034
GO:0033365 protein localization to organelle 603 154 0.0000036
GO:0006364 rRNA processing 117 44 0.0000044
GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 632 0.0000114
GO:0006351 transcription, DNA-templated 2952 599 0.0000132
GO:0044238 primary metabolic process 8725 1593 0.0000169
GO:0010468 regulation of gene expression 3465 690 0.0000196
GO:0071704 organic substance metabolic process 8974 1632 0.0000252
GO:0010556 regulation of macromolecule biosynthetic process 3214 643 0.0000270
GO:0044237 cellular metabolic process 8652 1576 0.0000375
GO:0031326 regulation of cellular biosynthetic process 3340 664 0.0000394
GO:0042274 ribosomal small subunit biogenesis 21 14 0.0000434
GO:0016032 viral process 674 161 0.0000611
GO:0044764 multi-organism cellular process 682 162 0.0000802
GO:0009889 regulation of biosynthetic process 3367 667 0.0001335
GO:0006355 regulation of transcription, DNA-templated 2851 574 0.0001695
GO:0016482 cytoplasmic transport 825 191 0.0002281
GO:0043933 macromolecular complex subunit organization 1450 312 0.0003452
GO:0051252 regulation of RNA metabolic process 2966 593 0.0003452
GO:2001141 regulation of RNA biosynthetic process 2888 578 0.0003898
GO:0044265 cellular macromolecule catabolic process 798 183 0.0008243
GO:0008152 metabolic process 9725 1741 0.0016519
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 165 0.0021430
GO:0044419 interspecies interaction between organisms 727 165 0.0021430
GO:0071822 protein complex subunit organization 1283 275 0.0027472
GO:0006396 RNA processing 676 154 0.0038339
GO:0042273 ribosomal large subunit biogenesis 16 10 0.0045692
GO:0009057 macromolecule catabolic process 983 214 0.0065449
GO:0006886 intracellular protein transport 758 169 0.0109497
GO:0000028 ribosomal small subunit assembly 7 6 0.0130063
GO:0034470 ncRNA processing 235 61 0.0169594
GO:1902582 single-organism intracellular transport 1181 247 0.0224227
GO:0070727 cellular macromolecule localization 1129 237 0.0419972

Under enriched (15)

category term numInCat numDEInCat q.value2
7483 GO:0002376 immune system process 1936 252 0.0048189
7482 GO:0022610 biological adhesion 916 111 0.0145399
7481 GO:0007155 cell adhesion 912 111 0.0145399
7480 GO:0001775 cell activation 767 86 0.0145399
7478 GO:0016337 single organismal cell-cell adhesion 283 24 0.0290844
7477 GO:0007599 hemostasis 485 51 0.0290844
7476 GO:0050817 coagulation 483 51 0.0290844
7479 GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 3 0.0290844
7470 GO:0023052 signaling 4496 687 0.0290844
7471 GO:0044700 single organism signaling 4496 687 0.0290844
7473 GO:0007596 blood coagulation 480 51 0.0290844
7472 GO:0006928 cellular component movement 1405 192 0.0290844
7468 GO:0007154 cell communication 4559 698 0.0290844
7474 GO:0098602 single organism cell adhesion 327 31 0.0290844
7469 GO:0040011 locomotion 1247 167 0.0290844
7465 GO:0042060 wound healing 595 69 0.0503501
7466 GO:0050900 leukocyte migration 271 23 0.0514254
7464 GO:0007165 signal transduction 4077 622 0.0525087
7461 GO:0006955 immune response 1137 146 0.0636357
7463 GO:0050878 regulation of body fluid levels 579 67 0.0636357

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)