Skip to main content

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
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us