Table 2. Network property of CRE co-occurrence networks and clique-clique networks of the input gene-sets.

The coefficient of assortativity (r) reflects the assortative mixing topology of a network. Negative values of r of the CRE co-occurrence networks indicate their disassortative mixing topology whereas, positive values of r observed in clique-clique networks imply their assortative mixing topology. Further, the network clustering coefficient ($\bar{C}$) values of the clique-clique networks are significantly higher than their respective CRE co-occurrence networks and this global attribute is an indicator of cohesiveness of the clique-clique networks. Significance is tested by permutation Mann-Whitney U test (No. of permutation = 10000), p < 0.001.

Input gene-set	Tissue	CRE co-occurrence network		clique-clique network
		r	$\bar{C}$	r	$\bar{C}$
WRKY	Leaf	-0.176	0.052	0.238	0.690
WRKY	Root	-0.176	0.127	0.504	0.684
MYB	Leaf	-0.131	0.118	0.536	0.725
MYB	Root	-0.161	0.134	0.094	0.775
ERF	Leaf	-0.138	0.165	0.433	0.675
ERF	Root	-0.104	0.127	0.439	0.622
NAC	Leaf	-0.007	0.086	0.627	0.435
NAC	Root	—	—	—	—
Defense response	Leaf	-0.116	0.211	0.273	0.828
Defense response	Root	-0.132	0.209	0.112	0.871
Response to stress	Leaf	-0.161	0.133	0.538	0.672
Response to stress	Root	-0.103	0.135	0.325	0.679
Chitin catabolic process	Leaf	-0.033	0.231	0.459	0.723
Chitin catabolic process	Root	—	—	—	—
GPCR signaling pathway	Leaf	-0.07	0.115	0.365	0.781
GPCR signaling pathway	Root	-0.006	0.237	0.313	0.721