Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes

Table 2

Conserved motifs identified in the promoter regions of hub genes using the MEME tool.

	Motif	-value	Motif width	Sites	Significant GO enriched terms; ( value<0.05)
1	NAVAAAAAAARAAARARAAARAAAAHMAA; Consensus sequence: [AGT]A[AG]AA[AC]AAAA[AG]A[AG][AG][AGC]A[AG]AA[AG][AG]A[AG]AA[ATC][AC]A[AGT]	2.8e-077	29	229	(i) GO:0042023: DNA endoreduplication; (ii) GO:0009944: Polarity specification of adaxial/abaxial axis; (iii) GO:0009735: Response to cytokinin stimulus; (iv) GO:0009744: Response to sucrose stimulus; (v) GO:0006468: Protein amino acid phosphorylation; (vi) GO:0009965: Leaf morphogenesis
	Consensus logo:
2	DTTTTTKTTTTKTTY; Consensus sequence: [AGT][TG]TTTT[TG]TTTT[TG][TG]T[TCG]	6.0e-020	15	245
	Consensus logo:
3	NDRRAGDDDRRWARRRARAGAADRRDAG; Consensus sequence: [AGC][GAT][AG][AG][AT][GA][AGT][ATG][AGT][GA][AG][AT]A[GA][AG][GAC]A[AG]A[GA]A[AG][GAT][AG][AG][GTA][AT][GT]	3.6e-025	28	121	(i) GO:0009944: Polarity specification of adaxial/abaxial axis; (ii) GO:0048481: Ovule development; (iii) GO:0010050: Vegetative phase change; (iv) GO:0010051: Xylem and phloem pattern formation; (v) GO:0042023: DNA endoreduplication; (vi) GO:0035196: Production of miRNAs involved in gene silencing by miRNA; (vii) GO:0009740: Gibberellic acid mediated signaling pathway
	Consensus logo:
4	CMAYCTYCTCCDTCHBCATC; Consensus sequence: [CT][CA]A[TC]CT[CT]CT[CT]C[TAG][TGC][CT][ATC][GTC]C[AT][TC]C	5.3e-007	20	44
	Consensus logo: