Table 1. Statistical parameters of CRE co-occurrence networks of the input gene-sets.

In the CRE co-occurrence network statistics, Nodes refer to the number of CREs present in the network and Edges correspond to the number of significantly co-occurring interactions. Cliques refers to the number of cliques obtained from each network. Clique size(k) refers to the size of cliques (number of nodes in each clique). All the CREs do not form cliques; here CREs in cliques refers to the number of CREs those appear in cliques.

Input gene-set	Tissue	No. of promoters	CRE co-occurrence network statistics
			Nodes	Edges	Cliques	Clique size (k)	CREs in cliques
WRKY	Leaf	20	110	260	38	3, 4	38
	Root	20	113	257	69	3	60
MYB	Leaf	18	112	247	47	3, 4	54
	Root	14	101	212	38	3, 4	47
ERF	Leaf	19	121	347	76	3, 4	97
	Root	23	118	261	44	3	55
NAC	Leaf	15	95	162	17	3, 4	31
	Root	6	—	—	—	—	—
Chitin catabolic process	Leaf	11	93	208	53	3, 4, 5	61
	Root	3	—	—	—	—	—
Response to stress	Leaf	23	122	351	97	3	73
	Root	12	90	210	45	3, 4	61
Defense response	Leaf	19	111	287	88	3, 4, 5	63
	Root	12	83	177	60	3, 4	47
GPCR signaling pathway	Leaf	26	122	291	48	3, 4	57
	Root	11	85	219	59	3, 4, 5, 6	54