This report has goseq results for fasting insulin when:

  1. Genes with FDR < 0.1 marked as DE
  2. Genes from above list with positive effect marked as differentially expressed
  3. Genes from above list with negative effect marked as differentially expressed

This report was generated on June 18 2015

Goseq results also saved in csv files located on snowwhite in directory: /net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/jun3/12junReps/csv

Step 1: Load in all the necessary data/libraries

library(goseq)

## Loading required package: BiasedUrn
## Loading required package: geneLenDataBase
## Loading required package: DBI

library(qvalue)

fName <- "/net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/traits/peer_k03_S_Insu_all_genes.txt"
outFile <- "S_Insu"

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 4431 DE genes with postive effect and 3889 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 (87)

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 167 125 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 88 0.0000000
GO:0006414 translational elongation 121 97 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 89 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 90 0.0000000
GO:0045047 protein targeting to ER 110 89 0.0000000
GO:0006415 translational termination 95 79 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 99 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 93 0.0000000
GO:0006612 protein targeting to membrane 171 120 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 123 0.0000000
GO:0019083 viral transcription 158 108 0.0000000
GO:0006955 immune response 1137 589 0.0000000
GO:0006401 RNA catabolic process 222 142 0.0000000
GO:0006402 mRNA catabolic process 196 128 0.0000001
GO:0019080 viral gene expression 168 110 0.0000005
GO:0044033 multi-organism metabolic process 178 115 0.0000007
GO:0002757 immune response-activating signal transduction 333 197 0.0000008
GO:0045321 leukocyte activation 561 307 0.0000015
GO:0046649 lymphocyte activation 480 267 0.0000022
GO:0043933 macromolecular complex subunit organization 1450 723 0.0000032
GO:0071822 protein complex subunit organization 1283 646 0.0000032
GO:0006412 translation 496 272 0.0000036
GO:0043624 cellular protein complex disassembly 174 111 0.0000055
GO:0043241 protein complex disassembly 195 122 0.0000058
GO:0002684 positive regulation of immune system process 610 324 0.0000220
GO:0016482 cytoplasmic transport 825 426 0.0000278
GO:0032984 macromolecular complex disassembly 205 124 0.0000351
GO:0050778 positive regulation of immune response 441 242 0.0000371
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 124 0.0000574
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 376 0.0000635
GO:0044419 interspecies interaction between organisms 727 376 0.0000635
GO:0002253 activation of immune response 373 208 0.0000700
GO:0072594 establishment of protein localization to organelle 456 246 0.0001092
GO:0090150 establishment of protein localization to membrane 296 167 0.0001545
GO:0001775 cell activation 767 392 0.0001773
GO:0002764 immune response-regulating signaling pathway 428 233 0.0002023
GO:1902578 single-organism localization 426 230 0.0002185
GO:1902580 single-organism cellular localization 426 230 0.0002185
GO:0019058 viral life cycle 303 169 0.0002290
GO:0045087 innate immune response 724 371 0.0003202
GO:0072657 protein localization to membrane 371 202 0.0003472
GO:0002376 immune system process 1936 925 0.0003726
GO:0033365 protein localization to organelle 603 314 0.0004331
GO:0050776 regulation of immune response 666 343 0.0006976
GO:0006605 protein targeting 497 262 0.0010010
GO:0044764 multi-organism cellular process 682 349 0.0010769
GO:0002252 immune effector process 504 264 0.0010785
GO:0016032 viral process 674 345 0.0011115
GO:0042110 T cell activation 347 189 0.0014197
GO:0002682 regulation of immune system process 997 494 0.0014959
GO:1902582 single-organism intracellular transport 1181 579 0.0019894
GO:0051249 regulation of lymphocyte activation 298 164 0.0022780
GO:0002694 regulation of leukocyte activation 340 184 0.0025861
GO:0098542 defense response to other organism 271 149 0.0035464
GO:0022411 cellular component disassembly 412 219 0.0037773
GO:0051251 positive regulation of lymphocyte activation 212 120 0.0059635
GO:0044802 single-organism membrane organization 638 324 0.0060422
GO:0042113 B cell activation 169 99 0.0064876
GO:0046651 lymphocyte proliferation 189 108 0.0076637
GO:0032943 mononuclear cell proliferation 191 109 0.0076638
GO:0050851 antigen receptor-mediated signaling pathway 138 83 0.0081546
GO:0002696 positive regulation of leukocyte activation 230 128 0.0081546
GO:0050867 positive regulation of cell activation 239 132 0.0098838
GO:0033036 macromolecule localization 2032 958 0.0101470
GO:0065003 macromolecular complex assembly 1091 531 0.0101470
GO:0006952 defense response 1178 565 0.0154983
GO:0070727 cellular macromolecule localization 1129 548 0.0154983
GO:0050865 regulation of cell activation 366 192 0.0180027
GO:0006886 intracellular protein transport 758 376 0.0205751
GO:0002274 myeloid leukocyte activation 123 73 0.0221505
GO:0034613 cellular protein localization 1124 544 0.0223561
GO:0002831 regulation of response to biotic stimulus 97 60 0.0227566
GO:0070661 leukocyte proliferation 200 111 0.0263323
GO:0061024 membrane organization 778 383 0.0313586
GO:0043207 response to external biotic stimulus 535 268 0.0321210
GO:0051707 response to other organism 535 268 0.0321210
GO:0042100 B cell proliferation 57 38 0.0338058
GO:0009607 response to biotic stimulus 566 282 0.0338058
GO:0050863 regulation of T cell activation 226 123 0.0338058
GO:0070271 protein complex biogenesis 934 454 0.0338058
GO:0031294 lymphocyte costimulation 63 41 0.0338058
GO:0031295 T cell costimulation 63 41 0.0338058
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 166 0.0347728
GO:0006968 cellular defense response 45 31 0.0361472
GO:0006417 regulation of translation 249 135 0.0426306
GO:0006461 protein complex assembly 932 452 0.0426306

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
10604 GO:0000904 cell morphogenesis involved in differentiation 701 260 1
10993 GO:0014821 phasic smooth muscle contraction 14 0 1
10605 GO:0007431 salivary gland development 36 6 1
11807 GO:0051383 kinetochore organization 13 0 1
10595 GO:0030030 cell projection organization 991 385 1
10597 GO:0045596 negative regulation of cell differentiation 440 158 1
10593 GO:0048858 cell projection morphogenesis 699 266 1
10589 GO:0000902 cell morphogenesis 993 386 1
10599 GO:0050679 positive regulation of epithelial cell proliferation 123 36 1
10601 GO:0048663 neuron fate commitment 38 7 1
10588 GO:0051093 negative regulation of developmental process 546 201 1
10586 GO:0032990 cell part morphogenesis 718 275 1
10602 GO:0060445 branching involved in salivary gland morphogenesis 23 3 1
11899 GO:0060395 SMAD protein signal transduction 11 0 1
10592 GO:0030510 regulation of BMP signaling pathway 61 15 1
11806 GO:0051382 kinetochore assembly 11 0 1
10590 GO:0048546 digestive tract morphogenesis 45 10 1
10591 GO:0035019 somatic stem cell maintenance 39 8 1
10596 GO:0007435 salivary gland morphogenesis 32 6 1
10577 GO:0032989 cellular component morphogenesis 1059 418 1

Positive Effect

Over enriched categories (195)

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 435 0.0000000
GO:0002376 immune system process 1936 647 0.0000000
GO:0045321 leukocyte activation 561 238 0.0000000
GO:0001775 cell activation 767 294 0.0000000
GO:0046649 lymphocyte activation 480 204 0.0000000
GO:0002757 immune response-activating signal transduction 333 151 0.0000000
GO:0050776 regulation of immune response 666 254 0.0000000
GO:0002684 positive regulation of immune system process 610 236 0.0000000
GO:0050778 positive regulation of immune response 441 183 0.0000000
GO:0002682 regulation of immune system process 997 350 0.0000000
GO:0006952 defense response 1178 399 0.0000000
GO:0045087 innate immune response 724 268 0.0000000
GO:0042110 T cell activation 347 150 0.0000000
GO:0002252 immune effector process 504 198 0.0000000
GO:0002253 activation of immune response 373 157 0.0000000
GO:0002429 immune response-activating cell surface receptor signaling pathway 204 97 0.0000000
GO:0002764 immune response-regulating signaling pathway 428 168 0.0000000
GO:0002694 regulation of leukocyte activation 340 137 0.0000000
GO:0098542 defense response to other organism 271 114 0.0000000
GO:0043207 response to external biotic stimulus 535 195 0.0000000
GO:0051707 response to other organism 535 195 0.0000000
GO:0009607 response to biotic stimulus 566 204 0.0000000
GO:0051249 regulation of lymphocyte activation 298 123 0.0000000
GO:0050865 regulation of cell activation 366 143 0.0000000
GO:0002274 myeloid leukocyte activation 123 62 0.0000000
GO:0050851 antigen receptor-mediated signaling pathway 138 68 0.0000000
GO:0032943 mononuclear cell proliferation 191 85 0.0000001
GO:0050863 regulation of T cell activation 226 96 0.0000001
GO:0006950 response to stress 2909 827 0.0000001
GO:0046651 lymphocyte proliferation 189 84 0.0000001
GO:0050896 response to stimulus 6126 1631 0.0000002
GO:0002443 leukocyte mediated immunity 211 90 0.0000002
GO:0070661 leukocyte proliferation 200 86 0.0000005
GO:0050900 leukocyte migration 271 108 0.0000005
GO:0044763 single-organism cellular process 9511 2441 0.0000005
GO:0050867 positive regulation of cell activation 239 98 0.0000006
GO:0001816 cytokine production 471 168 0.0000006
GO:0002696 positive regulation of leukocyte activation 230 95 0.0000006
GO:0002263 cell activation involved in immune response 141 66 0.0000008
GO:0002366 leukocyte activation involved in immune response 141 66 0.0000008
GO:0051251 positive regulation of lymphocyte activation 212 89 0.0000008
GO:0002768 immune response-regulating cell surface receptor signaling pathway 312 119 0.0000042
GO:0042113 B cell activation 169 74 0.0000042
GO:0045088 regulation of innate immune response 243 97 0.0000069
GO:0007165 signal transduction 4077 1108 0.0000084
GO:0050870 positive regulation of T cell activation 165 71 0.0000122
GO:0002697 regulation of immune effector process 231 91 0.0000187
GO:0042098 T cell proliferation 135 60 0.0000291
GO:0034097 response to cytokine 534 179 0.0000413
GO:0050853 B cell receptor signaling pathway 39 25 0.0000413
GO:0022904 respiratory electron transport chain 105 48 0.0000476
GO:0031294 lymphocyte costimulation 63 34 0.0000491
GO:0031295 T cell costimulation 63 34 0.0000491
GO:0048584 positive regulation of response to stimulus 1324 393 0.0000506
GO:0031347 regulation of defense response 462 157 0.0000633
GO:0022900 electron transport chain 106 48 0.0000633
GO:0001817 regulation of cytokine production 417 143 0.0000810
GO:0050670 regulation of lymphocyte proliferation 146 62 0.0001054
GO:0030098 lymphocyte differentiation 235 90 0.0001054
GO:0002275 myeloid cell activation involved in immune response 54 30 0.0001113
GO:0009615 response to virus 261 97 0.0001282
GO:0042742 defense response to bacterium 102 46 0.0001282
GO:0032944 regulation of mononuclear cell proliferation 147 62 0.0001320
GO:0070663 regulation of leukocyte proliferation 151 63 0.0001687
GO:0030595 leukocyte chemotaxis 130 55 0.0002162
GO:0009617 response to bacterium 298 106 0.0002884
GO:0019221 cytokine-mediated signaling pathway 345 121 0.0002987
GO:0050852 T cell receptor signaling pathway 106 48 0.0003127
GO:0042129 regulation of T cell proliferation 108 48 0.0003277
GO:0030217 T cell differentiation 167 68 0.0003347
GO:0072676 lymphocyte migration 47 26 0.0003381
GO:0045089 positive regulation of innate immune response 196 77 0.0003808
GO:0045333 cellular respiration 158 63 0.0003819
GO:0002521 leukocyte differentiation 353 123 0.0003833
GO:0060326 cell chemotaxis 177 69 0.0003833
GO:0023052 signaling 4496 1198 0.0004466
GO:0044700 single organism signaling 4496 1198 0.0004466
GO:0002703 regulation of leukocyte mediated immunity 109 48 0.0004568
GO:0044699 single-organism process 10471 2636 0.0004897
GO:0007154 cell communication 4559 1213 0.0004917
GO:0071345 cellular response to cytokine stimulus 452 151 0.0005419
GO:0002831 regulation of response to biotic stimulus 97 44 0.0005977
GO:0006968 cellular defense response 45 25 0.0006482
GO:0031349 positive regulation of defense response 259 94 0.0007288
GO:0045576 mast cell activation 40 23 0.0007288
GO:0042102 positive regulation of T cell proliferation 70 34 0.0007894
GO:0051607 defense response to virus 173 68 0.0007944
GO:0006119 oxidative phosphorylation 70 33 0.0009690
GO:0050817 coagulation 483 159 0.0009753
GO:0043299 leukocyte degranulation 43 24 0.0009753
GO:0002444 myeloid leukocyte mediated immunity 54 28 0.0009860
GO:0001819 positive regulation of cytokine production 245 89 0.0011018
GO:0007599 hemostasis 485 159 0.0012000
GO:0042100 B cell proliferation 57 29 0.0012969
GO:0097530 granulocyte migration 71 33 0.0013545
GO:0007596 blood coagulation 480 157 0.0015766
GO:0070271 protein complex biogenesis 934 280 0.0015817
GO:0090382 phagosome maturation 42 23 0.0016910
GO:1990266 neutrophil migration 57 28 0.0017624
GO:0045055 regulated secretory pathway 55 28 0.0018166
GO:0043900 regulation of multi-organism process 273 96 0.0018794
GO:0048518 positive regulation of biological process 3684 985 0.0021286
GO:0002758 innate immune response-activating signal transduction 160 63 0.0021354
GO:0002218 activation of innate immune response 167 65 0.0023572
GO:0006461 protein complex assembly 932 278 0.0024243
GO:0050864 regulation of B cell activation 82 37 0.0027868
GO:0006954 inflammatory response 473 151 0.0029983
GO:0009605 response to external stimulus 1589 449 0.0033689
GO:0030593 neutrophil chemotaxis 56 27 0.0034207
GO:0002449 lymphocyte mediated immunity 163 62 0.0034207
GO:0051716 cellular response to stimulus 4976 1303 0.0034707
GO:0048583 regulation of response to stimulus 2704 737 0.0035239
GO:0002448 mast cell mediated immunity 28 17 0.0036073
GO:0002279 mast cell activation involved in immune response 28 17 0.0036073
GO:0032615 interleukin-12 production 41 22 0.0040882
GO:0002683 negative regulation of immune system process 198 73 0.0046442
GO:0006909 phagocytosis 162 62 0.0048907
GO:0050777 negative regulation of immune response 60 29 0.0048907
GO:0070665 positive regulation of leukocyte proliferation 100 42 0.0048907
GO:0002221 pattern recognition receptor signaling pathway 158 61 0.0048907
GO:0035987 endodermal cell differentiation 38 21 0.0048907
GO:0010033 response to organic substance 2043 565 0.0051696
GO:0007166 cell surface receptor signaling pathway 2374 650 0.0057638
GO:0071621 granulocyte chemotaxis 67 30 0.0057885
GO:0050830 defense response to Gram-positive bacterium 38 20 0.0070611
GO:0036336 dendritic cell migration 22 14 0.0071797
GO:0097529 myeloid leukocyte migration 104 42 0.0071797
GO:0065003 macromolecular complex assembly 1091 316 0.0073868
GO:0043303 mast cell degranulation 27 16 0.0081082
GO:0002250 adaptive immune response 194 70 0.0081082
GO:0032655 regulation of interleukin-12 production 40 21 0.0081082
GO:0051701 interaction with host 105 43 0.0086450
GO:0002699 positive regulation of immune effector process 109 44 0.0086835
GO:0042060 wound healing 595 184 0.0088853
GO:0009620 response to fungus 23 14 0.0093261
GO:0036230 granulocyte activation 25 15 0.0095496
GO:0050688 regulation of defense response to virus 71 32 0.0097363
GO:0042773 ATP synthesis coupled electron transport 54 25 0.0099467
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 25 0.0099467
GO:0050671 positive regulation of lymphocyte proliferation 97 40 0.0099467
GO:0002407 dendritic cell chemotaxis 18 12 0.0101170
GO:0002706 regulation of lymphocyte mediated immunity 85 36 0.0104253
GO:0032946 positive regulation of mononuclear cell proliferation 98 40 0.0127904
GO:0007159 leukocyte cell-cell adhesion 44 22 0.0127904
GO:0002704 negative regulation of leukocyte mediated immunity 18 12 0.0127948
GO:0001706 endoderm formation 46 23 0.0127948
GO:0032648 regulation of interferon-beta production 35 19 0.0130520
GO:0034341 response to interferon-gamma 108 43 0.0131638
GO:0006915 apoptotic process 1521 425 0.0136138
GO:0006091 generation of precursor metabolites and energy 394 125 0.0147629
GO:0048247 lymphocyte chemotaxis 24 14 0.0147632
GO:0042221 response to chemical 2788 746 0.0153990
GO:0012501 programmed cell death 1539 429 0.0154654
GO:0001906 cell killing 75 32 0.0156698
GO:0001909 leukocyte mediated cytotoxicity 66 29 0.0173814
GO:0070098 chemokine-mediated signaling pathway 37 19 0.0178698
GO:0016265 death 1755 484 0.0181512
GO:0008219 cell death 1751 483 0.0182004
GO:0048522 positive regulation of cellular process 3307 877 0.0182310
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 40 0.0194190
GO:0030889 negative regulation of B cell proliferation 14 10 0.0201932
GO:0007005 mitochondrion organization 298 98 0.0204383
GO:0015671 oxygen transport 11 8 0.0223618
GO:0071350 cellular response to interleukin-15 10 8 0.0279742
GO:0042119 neutrophil activation 22 13 0.0289191
GO:0032729 positive regulation of interferon-gamma production 35 18 0.0290498
GO:0002228 natural killer cell mediated immunity 38 19 0.0290762
GO:0042267 natural killer cell mediated cytotoxicity 38 19 0.0290762
GO:0032608 interferon-beta production 37 19 0.0295316
GO:0006611 protein export from nucleus 49 23 0.0320281
GO:0009306 protein secretion 183 64 0.0321693
GO:0002224 toll-like receptor signaling pathway 136 51 0.0321693
GO:1902105 regulation of leukocyte differentiation 178 63 0.0330128
GO:0002237 response to molecule of bacterial origin 214 73 0.0355732
GO:0002440 production of molecular mediator of immune response 103 40 0.0355914
GO:0032609 interferon-gamma production 78 32 0.0356669
GO:1902107 positive regulation of leukocyte differentiation 99 39 0.0359175
GO:0002698 negative regulation of immune effector process 61 27 0.0367588
GO:0002431 Fc receptor mediated stimulatory signaling pathway 73 31 0.0367588
GO:0032607 interferon-alpha production 17 11 0.0367588
GO:0050871 positive regulation of B cell activation 50 23 0.0372015
GO:0002532 production of molecular mediator involved in inflammatory response 25 14 0.0381152
GO:0006928 cellular component movement 1405 391 0.0394647
GO:0032728 positive regulation of interferon-beta production 22 13 0.0411559
GO:0045785 positive regulation of cell adhesion 149 54 0.0424905
GO:0050663 cytokine secretion 108 41 0.0433924
GO:0009611 response to wounding 833 241 0.0434674
GO:0045577 regulation of B cell differentiation 20 12 0.0434674
GO:0043623 cellular protein complex assembly 352 111 0.0471446
GO:0042116 macrophage activation 39 19 0.0483606
GO:0065008 regulation of biological quality 2575 686 0.0487769
GO:0006986 response to unfolded protein 133 49 0.0491067
GO:0007492 endoderm development 62 27 0.0491915
GO:0008089 anterograde axon cargo transport 23 13 0.0492072
GO:0016310 phosphorylation 1655 455 0.0496001

Under enriched (36)

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
12747 GO:0016070 RNA metabolic process 3693 755 0.0000000
9120 GO:0032774 RNA biosynthetic process 3063 616 0.0000021
9119 GO:0090304 nucleic acid metabolic process 4166 873 0.0000085
9118 GO:0034654 nucleobase-containing compound biosynthetic process 3350 688 0.0000130
9117 GO:1901362 organic cyclic compound biosynthetic process 3503 727 0.0000327
9116 GO:0010467 gene expression 4322 920 0.0000792
9115 GO:0006355 regulation of transcription, DNA-templated 2851 584 0.0000797
9114 GO:0019438 aromatic compound biosynthetic process 3410 711 0.0000797
9113 GO:0018130 heterocycle biosynthetic process 3413 712 0.0000797
9112 GO:0006351 transcription, DNA-templated 2952 609 0.0001046
9111 GO:0034645 cellular macromolecule biosynthetic process 3920 833 0.0001479
9110 GO:0044271 cellular nitrogen compound biosynthetic process 3463 727 0.0001479
9109 GO:2001141 regulation of RNA biosynthetic process 2888 597 0.0001568
9108 GO:0051252 regulation of RNA metabolic process 2966 617 0.0002468
9107 GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 656 0.0003301
9106 GO:1901360 organic cyclic compound metabolic process 5728 1263 0.0003301
9105 GO:0006807 nitrogen compound metabolic process 6075 1353 0.0011159
9104 GO:0006139 nucleobase-containing compound metabolic process 5435 1201 0.0013430
9102 GO:0009059 macromolecule biosynthetic process 4025 870 0.0015481
9101 GO:0010468 regulation of gene expression 3465 742 0.0019541
9100 GO:0046483 heterocycle metabolic process 5565 1235 0.0019942
9099 GO:0006725 cellular aromatic compound metabolic process 5569 1236 0.0019942
9098 GO:0034641 cellular nitrogen compound metabolic process 5755 1283 0.0031406
9103 GO:0006415 translational termination 95 6 0.0043118
9097 GO:0019219 regulation of nucleobase-containing compound metabolic process 3668 796 0.0052289
9096 GO:0031326 regulation of cellular biosynthetic process 3340 719 0.0057717
9095 GO:0010556 regulation of macromolecule biosynthetic process 3214 690 0.0057717
9093 GO:0009889 regulation of biosynthetic process 3367 728 0.0097664
9094 GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 9 0.0174442
9092 GO:0072599 establishment of protein localization to endoplasmic reticulum 111 10 0.0262963
9089 GO:0044249 cellular biosynthetic process 4756 1060 0.0281181
9088 GO:0009058 biosynthetic process 4899 1094 0.0287064
9091 GO:0045047 protein targeting to ER 110 10 0.0288860
9090 GO:0006613 cotranslational protein targeting to membrane 109 10 0.0325938
9086 GO:0051171 regulation of nitrogen compound metabolic process 3754 828 0.0366597
9085 GO:1901576 organic substance biosynthetic process 4830 1080 0.0374136

Negative Effect

Over enriched categories (76)

category term numInCat numDEInCat q.value
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 79 0.0000000
GO:0006415 translational termination 95 73 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 80 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 79 0.0000000
GO:0045047 protein targeting to ER 110 79 0.0000000
GO:0006414 translational elongation 121 82 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 79 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 82 0.0000000
GO:0006413 translational initiation 167 95 0.0000000
GO:0006612 protein targeting to membrane 171 91 0.0000000
GO:0019083 viral transcription 158 85 0.0000000
GO:0019080 viral gene expression 168 85 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 90 0.0000000
GO:0044033 multi-organism metabolic process 178 86 0.0000000
GO:0006402 mRNA catabolic process 196 93 0.0000000
GO:0006401 RNA catabolic process 222 99 0.0000000
GO:0043624 cellular protein complex disassembly 174 83 0.0000000
GO:0043241 protein complex disassembly 195 88 0.0000000
GO:0032984 macromolecular complex disassembly 205 88 0.0000000
GO:0090150 establishment of protein localization to membrane 296 110 0.0000000
GO:0019058 viral life cycle 303 109 0.0000000
GO:0072657 protein localization to membrane 371 124 0.0000000
GO:0016070 RNA metabolic process 3693 841 0.0000000
GO:0006412 translation 496 151 0.0000000
GO:0090304 nucleic acid metabolic process 4166 930 0.0000000
GO:0032774 RNA biosynthetic process 3063 708 0.0000000
GO:0022411 cellular component disassembly 412 132 0.0000000
GO:0016071 mRNA metabolic process 615 178 0.0000000
GO:0034654 nucleobase-containing compound biosynthetic process 3350 758 0.0000001
GO:0072594 establishment of protein localization to organelle 456 138 0.0000002
GO:0018130 heterocycle biosynthetic process 3413 769 0.0000002
GO:1901362 organic cyclic compound biosynthetic process 3503 786 0.0000002
GO:1902578 single-organism localization 426 131 0.0000002
GO:1902580 single-organism cellular localization 426 131 0.0000002
GO:0034645 cellular macromolecule biosynthetic process 3920 869 0.0000002
GO:0022613 ribonucleoprotein complex biogenesis 280 93 0.0000004
GO:0010467 gene expression 4322 945 0.0000004
GO:0019438 aromatic compound biosynthetic process 3410 765 0.0000004
GO:0044271 cellular nitrogen compound biosynthetic process 3463 773 0.0000007
GO:0009059 macromolecule biosynthetic process 4025 884 0.0000008
GO:0044802 single-organism membrane organization 638 179 0.0000008
GO:0042254 ribosome biogenesis 167 62 0.0000013
GO:0006605 protein targeting 497 144 0.0000021
GO:0016072 rRNA metabolic process 122 49 0.0000027
GO:0044249 cellular biosynthetic process 4756 1016 0.0000069
GO:0009058 biosynthetic process 4899 1043 0.0000069
GO:1901576 organic substance biosynthetic process 4830 1029 0.0000081
GO:0006364 rRNA processing 117 46 0.0000140
GO:0033365 protein localization to organelle 603 165 0.0000150
GO:0061024 membrane organization 778 204 0.0000171
GO:0042274 ribosomal small subunit biogenesis 21 14 0.0001998
GO:0016032 viral process 674 174 0.0002729
GO:0044764 multi-organism cellular process 682 175 0.0003773
GO:0006807 nitrogen compound metabolic process 6075 1262 0.0004082
GO:1901360 organic cyclic compound metabolic process 5728 1195 0.0004850
GO:0016482 cytoplasmic transport 825 208 0.0005435
GO:0044260 cellular macromolecule metabolic process 6484 1335 0.0009567
GO:0043170 macromolecule metabolic process 7144 1458 0.0013879
GO:0046483 heterocycle metabolic process 5565 1159 0.0016735
GO:0006139 nucleobase-containing compound metabolic process 5435 1133 0.0022979
GO:0043933 macromolecular complex subunit organization 1450 337 0.0032764
GO:0034641 cellular nitrogen compound metabolic process 5755 1190 0.0041352
GO:0006725 cellular aromatic compound metabolic process 5569 1154 0.0048338
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 179 0.0048338
GO:0044419 interspecies interaction between organisms 727 179 0.0048338
GO:0044265 cellular macromolecule catabolic process 798 195 0.0092670
GO:0071822 protein complex subunit organization 1283 298 0.0124475
GO:0006396 RNA processing 676 166 0.0129358
GO:0042273 ribosomal large subunit biogenesis 16 10 0.0129460
GO:2000112 regulation of cellular macromolecule biosynthetic process 3129 672 0.0180276
GO:0034660 ncRNA metabolic process 325 86 0.0230600
GO:0000028 ribosomal small subunit assembly 7 6 0.0269092
GO:0006351 transcription, DNA-templated 2952 634 0.0277829
GO:0006886 intracellular protein transport 758 183 0.0288778
GO:0010556 regulation of macromolecule biosynthetic process 3214 684 0.0364415
GO:0034470 ncRNA processing 235 65 0.0364415

Under enriched (9)

category term numInCat numDEInCat q.value2
7931 GO:0002376 immune system process 1936 278 0.0002974
7930 GO:0006955 immune response 1137 154 0.0084389
7929 GO:0001775 cell activation 767 98 0.0146357
7928 GO:0006952 defense response 1178 166 0.0402827
7925 GO:0007154 cell communication 4559 783 0.0402827
7926 GO:0045321 leukocyte activation 561 69 0.0402827
7922 GO:0023052 signaling 4496 773 0.0402827
7923 GO:0044700 single organism signaling 4496 773 0.0402827
7927 GO:0019882 antigen processing and presentation 215 18 0.0402827
7920 GO:0007165 signal transduction 4077 697 0.0558204
7919 GO:0006928 cellular component movement 1405 220 0.0617560
7915 GO:0050896 response to stimulus 6126 1075 0.0677796
7917 GO:0040011 locomotion 1247 192 0.0677796
7924 GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 5 0.0815120
7913 GO:0050776 regulation of immune response 666 89 0.0815120
7918 GO:0048002 antigen processing and presentation of peptide antigen 180 15 0.0815120
7914 GO:0042110 T cell activation 347 39 0.0815120
7911 GO:0002682 regulation of immune system process 997 144 0.1006474
7921 GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I 79 3 0.1232032
7912 GO:0019884 antigen processing and presentation of exogenous antigen 167 14 0.1348572

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)