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

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

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]

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.