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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