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Table 1 Modules identified in the network and their top over-represented Biological process GO terms

From: Large-scale gene co-expression network as a source of functional annotation for cattle genes

Module # probes # genes GO term Genes in GO terma p–valueb
Turquoise 2569 2050 system process 241/652 3.30E-31
Blue 806 690 nucleic acid metabolic process 211/2322 6.89E-10
Brown 606 526 organic acid metabolic process 113/565 1.38E-36
Yellow 566 521 RNA processing 83/455 6.26E-26
Green 557 471 RNA metabolic process 151/2064 3.36E-09
Red 519 431 cell cycle process 117/604 4.93E-50
Black 454 384 negative regulation of peptidase activity 22/129 2.76E-07
Pink 348 304 RNA metabolic process 117/2064 7.20E-17
Magenta 292 267 gene expression 111/2568 1.56E-08
Purple 275 361 ribonucleoprotein complex biogenesis 44/266 3.10E-24
Green yellow 271 214 chromatin modification 26/336 3.79E-07
Tan 269 225 anatomical structure morphogenesis 72/1323 9.65E-14
Salmon 239 216 translation 85/398 1.40E-67
Cyan 202 181 oxidation-reduction process 35/619 1.15E-08
Midnight blue 200 191 hydrogen ion transmembrane transport 14/60 1.14E-10
Light cyan 188 151 leukocyte activation 34/365 7.29E-20
Grey60 184 158 leukocyte activation 30/365 3.28E-13
Light green 169 160 purine ribonucleoside triphosphate metabolic process 17/133 2.08E-09
Light yellow 165 149 sterol biosynthetic process 15/31 2.21E-18
Royal blue 164 146 mitochondrial translation 8/43 9.87E-06
Dark red 158 139 proteasomal protein catabolic process 12/245 6.00E-3
Dark green 146 128 response to endoplasmic reticulum stress 15/146 2.23E-09
Dark turquoise 120 88 tricarboxylic acid metabolic process 3/27 5.75E-3
Dark grey 102 80 inflammatory response 28/269 1.40E-23
Orange 98 78 antigen processing and presentation of peptide antigen 12/26 1.00E-18
Dark orange 95 85 regulation of mRNA metabolic process 3/69 1.40E-2
White 80 63 defense response to virus 15/138 4.68E-15
Sky blue 67 53 transcription from RNA polymerase I promoter 3/32 4.91E-4
Saddle brown 62 53 defense response to bacterium 7/94 1.16E-11
Steel blue 61 48 acute inflammatory response 6/46 7.97E-07
Pale turquoise 34 24 L-serine metabolic process 3/7 2.55E-06
Violet 29 23 amino acid activation 7/36 1.84E-12
  1. aThe two values listed in this column refer to the number of genes associated with the over-represented GO term in the module and the number of genes associated with the same GO term in Affymetrix Genechip Bovine Genome Array
  2. bThe p-value indicated the probability that a module contains equal or larger number of genes associated with the GO term under a hypergeometric distribution after Bonferroni step-down correction