Table 3. Details of the stochastic simulations performed to analyse the impact of the CTCF binding site, isochores, cryptic RSSs, and DNase hypersensitive sites on the edge distribution.

Formula	Iterations	Estimate	Std. Error	p-value
edges + nodecov("dnase")	100	0.86291	0.07961	<1e-04
edges + nodecov("ctcf")	100	0.52386	0.04158	<1e-04
edges + nodecov("rss")	100	0.39780	0.03176	<1e-04
edges + nodecov("iso")	100	-0.84035	0.09269	<1e-04

As the summary table shows, after 100 iterations the statistics achieved a high degree of confidence (P-value < 0.0001). In particular, data demonstrate that DNase hypersensitive sites and CTCF binding sites have a positive influence on the presence of edges (nodecov.dnase = 0.86291 ± 0.07961 and nodecov.ctcf = 0.52386 ± 0.04158); at the same way cryptic RSSs are positively correlated with edges (nodecov.rss = 0.39780 ± 0.03176) although with less impact; on the other hand, isochores are negatively correlated with the edge distribution (nodecov.iso = -0.84035 ± 0.09269).