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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.