Table 1.

Correlating Properties with Centrality and Hierarchy Height

Category	Property	Correlation with
		Degree centrality^		Betweenness centrality		$\frac{\mathbf{O}-\mathbf{I}}{\mathbf{O}+\mathbf{I}}$
		Full	TF-TF	Full	TF-TF	TF-TF
Topology	# of TF partners in PPI	0.28**	0.27**	0.25*	0.33**	0.08
	# of miRNA regulators	0.24*	0.33**	−0.02	0.00	0.29**
	# of ncRNA targets	0.65**	0.49**	0.34**	0.35**	0.22*
	# of miRNA targets	0.62**	0.50**	0.33**	0.34**	0.19*
	# of distal targets	0.32**	0.24*	0.19*	0.23*	0.07
Dynamics	Amount of rewiring	−0.14	−0.12	0.44*	0.35	−0.42*
Expression	Expression level	0.14	0.12	0.23*	0.27*	−0.04
	Binding-exp. corr.	0.41**	0.31**	0.30**	0.36**	0.19*
Selection properties for factors	ns SNP density	−0.19*	−0.27*	−0.01	−0.03	−0.22
	Allelicity	0.20	0.28*	−0.10	−0.16	0.18
Selection properties for targets	ns SNP density	−0.05**
	dN/dS	−0.05**

Spearman correlation values of various properties (topological, dynamic, expression-related, and selection-related) with centrality measures and hierarchy height (h). Only properties which are significantly correlated with centrality or h are listed (* for P<0.05 and ** for P<0.01). For a full set of properties, p-values, and explanations, see Tables S4 and S6. Degree centrality (note ^{^}) refers to out-degree, except for selection properties on targets, in which case it refers to in-degree. In particular, out-degree in the full TF-target network refers to the “Targets” column in Table S4a, and the same quantity is used throughout Fig. 2.