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Table 2 Significantly enriched GO terms in AGCN modules (I = 1.8)

From: Arabidopsis gene co-expression network and its functional modules

module

# annotated genes1

GO term2

genes in GO term3

p value4

1

1208

photosynthesis

97/107

1.38E-52

2

684

response to oxidative stress

30/88

1.43E-07

3

438

protein biosynthesis

95/204

5.68E-52

4

256

DNA metabolism

59/107

9.07E-52

5

104

defense response

18/205

4.79E-08

6

87

reproductive structure development

15/100

3.16E-11

7

78

protein ubiquitination

5/14

1.00E-06

8

59

defense response

19/205

1.65E-13

9

48

establishment and/or maintenance of chromatin architecture

6/43

1.71E-06

11

39

cell wall modification

5/32 2

64E-06

15

36

response to wounding

7/54

4.50E-08

18

33

cuticle biosynthesis

5/8

3.45E-10

21

29

toxin metabolism

5/25

1.54E-07

27

23

glucosinolate biosynthesis

4/9

3.12E-08

28

18

RNA processing

5/65

1.65E-06

31

20

monosaccharide metabolism

5/47

5.67E-07

33

17

response to heat

10/47

1.69E-17

34

18

secondary cell wall biosynthesis (sensu Magnoliophyta)

6/8

1.51E-14

35

17

protein biosynthesis

11/204

1.75E-12

41

16

enzyme linked receptor protein signaling pathway

5/51

2.49E-07

42

15

organic acid metabolism

9/186

2.38E-10

43

13

response to auxin stimulus

7/69

6.62E-11

46

14

lipid metabolism

7/194

1.93E-07

50

12

cellular respiration

6/15

1.34E-13

56

11

leaf development

4/28

1.87E-07

67

10

starch metabolism

8/20

3.18E-19

79

9

indoleacetic acid metabolism

3/4

1.28E-08

80

8

phenylpropanoid metabolism

6/44

5.71E-12

119

6

response to heat

6/47

3.14E-13

122

6

lipid transport

4/47

7.49E-08

140

5

nitrogen compound metabolism

5/129

7.23E-09

154

4

wax biosynthesis

2/7

8.65E-06

165

4

glutamate biosynthesis

2/2 4

12E-07

170

4

electron transport

4/219

2.64E-06

173

4

fatty acid beta-oxidation

2/9

1.48E-05

180

4

purine transport

2/3

1.24E-06

190

4

response to water deprivation

4/41

2.87E-09

201

2

Glycolysis

2/16

8.24E-06

205

3

RNA splicing, via transesterification reactions with bulged adenosine as nucleophile

2/5

2.06E-06

213

4

response to heat

4/47

5.05E-09

224

3

fatty acid beta-oxidation

2/9

7.41E-06

238

3

sulfolipid biosynthesis

2/2

2.06E-07

266

3

ovule development

2/12

1.36E-05

273

3

phenylpropanoid metabolism

3/44

5.06E-07

311

3

Proteolysis

3/130

1.37E-05

315

3

response to iron ion

2/3

6.18E-07

  1. 1. The number of genes which were assigned with biological process GO terms in a module.
  2. 2. Only the most over-represented GO term was listed for each module.
  3. 3. The 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 the network.
  4. 4. The p value indicated the probability that a module contains equal or larger number of genes associated with the GO term under a hypergeometric distribution.