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Table 2 The 10 modules based on overlapping genes and some of their evidence supports

From: Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

Module Representative enriched biological process* Gene number Coherence (%)+ I$ M& L#
1 gibberellic acid mediated signaling pathway 57 7   √ [32]
2 polyamine biosynthetic process 52 4   √ [33]
3 flavonoid biosynthetic process 48 6   √ [34]
4 cytokinin biosynthetic process 35 3   √ [35]
5 Nodulation 28 7
6 regulation of cytoskeleton organization 32 3   
7 pattern specification process 11 9   
8 response to stress 34 9   √ [36]
9 response to UV-B 13 8 √ [37]
10 nitrile biosynthetic process 44 2   √ [38]
  1. Column 1 lists id of the module. Column 2* reports the representative enriched GO biological processes in these modules. Column 3 is the number of genes in the corresponding GO lists. Column 4 is the percent of genes in each module participating in the biological process, and + presents all of the GO biological processes in Table 2 with the significance p < 0.05. Column 5 (I$) shows if there are at least two predicted TFs in the module existing the interaction relation according to the STRING prediction and the BLAST homology search. Column 6 (M&) reports if the DNA binding motifs of some predicted TF families matched the motifs extracted from the upstream sequences of the regulated genes in the modules. Column 7 (L#) lists if previous literature had reported the relationship between the nodule development or formation and the gene function of the module.