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Table 1 32 Gene regulatory modules with high correlation coefficients and other supports

From: Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

Correlation coefficient

Most enriched biological process*

TF

Gene

Coherence†

I$

M&

L#

0.989913

lipid transport

7

62

6

Ce

√

√[27]

0.945372

positive regulation of release of sequestered calcium ion into cytosol

7

11

36

  

√[36]

0.930583

vegetative to reproductive phase transition of meristem

8

161

3

Ce

√

√[37, 38]

0.926575

proteolysis

8

27

18

E

√

√[39]

0.910277

steroid biosynthetic process

7

81

3

 

√

√[40]

0.902439

photosynthesis

9

114

12

T

 

√[41]

0.898638

protein transport

9

183

8

Ce

√

 

0.896121

regulation of cell shape

8

50

6

E&H

  

0.893346

ATP-dependent chromatin remodeling

6

163

1

E

√

 

0.890829

photosynthesis, light harvesting

11

102

12

 

√

√[41]

0.888479

mRNA processing

9

218

7

Ce

√

 

0.882899

translational elongation

9

85

4

E

√

 

0.880672

regulation of flower development

9

57

7

Ce

√

√[42]

0.867582

lipid transport

7

63

6

Ce

√

 

0.862264

skeletal system morphogenesis

9

70

4

T

√

 

0.857502

translation

11

125

12

Ce

  

0.855305

carotenoid biosynthetic process

9

103

3

Ce

√

 

0.852366

lactate metabolic process

7

84

4

E,T&H

√

 

0.843827

establishment or maintenance of polarity of embryonic epithelium

5

99

6

E

√

 

0.841523

flavonoid biosynthetic process

8

44

6

E

√

√[29]

0.836985

base-excision repair

10

36

8

E

  

0.830088

flavonoid biosynthetic process

9

38

15

E&T

√

√[29]

0.826087

acetyl-CoA biosynthetic process

7

158

3

E

 

√[43]

0.824363

auxin mediated signaling pathway

12

76

5

E

√

√[44]

0.820377

carbohydrate metabolic process

9

71

11

T

 

√[45]

0.817311

transcription

9

56

25

E

√

 

0.81347

superoxide metabolic process

10

46

6

T

  

0.812358

nodulation

10

73

4

E

√

√[28]

0.809849

PSII associated light-harvesting complex II catabolic process

8

108

2

E&Ce

√

√[45]

0.808305

metabolic process

7

44

13

T

√

 

0.806202

secondary cell wall biogenesis

8

97

6

E

√

√[46]

0.804089

DNA replication initiation

10

96

4

Ce

√

 
  1. Column 1 lists the average of the pairwise Pearson’s correlation coefficients of expression values of genes in these modules. Column 2* reports the most significantly enriched GO biological process in each module that has the smallest p-value. Column 3 lists the number of TFs predicted for a module. Column 4 lists the number of genes in a module that had GO annotations. Column 5† lists the percent of genes in each module participating in the biological process. Column 6 (I$) shows if at least two predicted TFs in a module interacted according to the STRING predictions and the BLAST homology search. Evidence sources for STRING predictions include E - experiments; Ce - co-expression; T – text mining; H - homology. Column 7 (M&) reports if the DNA binding motifs of some predicted TF families in a module matched the motifs extracted from the upstream sequences of the regulated genes in the module. Column 8 (L#) lists if previous literature had reported a relationship amongst at least one predicted TF family, a stress condition, and the predicted gene function of a module.