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Table 1 Selected gene modules identified from the network

From: Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response

Category

Module no.

Number of genes within the module

Percentage of genes sharing conserved interactions with Arabidopsis

Module annotation

Selected genes from the modulea

Enriched GO term

pValue

Cell Organization

49

71

80.28%

chromatin organization

his2a1/his2b1/his2b2/pcna2

nucleosome organization

2.15E-132

60

59

44.07%

cell division

cyc1/hmg9/GRMZM2G061287(CYCB2;4)

cell division

1.32E-07

64

58

63.79%

DNA replication

rfa1/rrb3/GRMZM2G139894(MCM2)

DNA replication

3.16E-39

69

53

30.19%

cytoskeleton

krp2/krp4/krp8/cyc3/cyc8

microtubule motor activity

1.64E-46

Development

6

182

35.71%

seed maturation

ole1/ole3/vp1

monolayer-surrounded lipid storage body

1.75E-10

16

139

12.95%

inflorescences development

ra1/ba1/ra3/spi1/tb1/bd1/yab10

abaxial cell fate specification

5.25E-10

46

73

2.74%

kernels development

o2/pbf1/az19D2/az19D1/de30/zp1/zp22.1

nutrient reservoir activity

6.32E-64

48

72

1.39%

ligules development

lg1/sbp28/ns1/myb43/sbp3

DNA binding

9.53E-06

210

15

60.00%

ligules development

knox3/kn1/rs1/hb123/lg3/lg4/hb76/ hb8/hb48/gn1/knox5

sequence-specific DNA binding

8.77E-17

Nutrients

36

88

23.86%

response to phosphate starvations

ppck2/ppck3/ppck4/pht7

cellular response to phosphate starvation

9.62E-17

72

51

43.14%

nitrate assimilation

nii2/nnr1/gln3/gln6

nitrate assimilation

1.18E-09

Primary Metabolism

14

151

18.54%

respiratory electron transport chain

GRMZM2G450825(COX1)/ GRMZM2G173833(COX2)

mitochondrion

9.10E-92

20

130

69.23%

photosynthesis

cyb6/GRMZM2G448174(PETA)/ GRMZM2G433927(PSBE)

photosynthesis

5.46E-30

86

40

42.50%

mitochondrial electron transport / ATP synthesis

nad1/nad4/GRMZM2G156068(ATP5)

mitochondrial membrane

9.35E-28

129

26

65.38%

photosynthesis

gpa1/lhcb2/lhcb3/lhcb7

photosynthesis

1.69E-38

Secondary Metabolism

40

84

27.38%

wax biosynthesis

gl1/gl2/gl3/fdl1

wax biosynthetic process

2.25E-13

65

57

29.82%

flavonoids biosynthesis

pr1/c2/whp1/chi1

flavonoid metabolic process

1.89E-12

73

49

42.86%

fatty acid biosynthesis

wri1/wri2/acc1/acc2

monocarboxylic acid metabolic process

2.64E-27

80

43

6.98%

benzoxazinoids and oxylipins biosynthesis

bx1/bx2/bx3/bx4/bx5/lox2/lox3/lox5/lox10

oxylipin metabolic process

6.12E-12

154

20

30.00%

flavonoids biosynthesis

bz2/a1/bz1/a2/r1

flavonoid biosynthetic process

2.26E-08

Stress

5

188

15.96%

response to fungus

nactf7/chn1/chn2/sip1

defense response to fungus, incompatible interaction

3.27E-09

10

157

47.13%

response to heat stress

hsp18c/hsp18f/hsp1/hsftf8/hsftf12

response to heat

8.75E-49

95

35

65.71%

response to endoplasmic reticulum stress

bip1/bip2/der1/bzip60

response to endoplasmic reticulum stress

6.89E-15

  1. aShown in parenthesis are the maize genes’ homologues in Arabidopsis