Fig. 3.

Enrichment of positive feedback and high-feedback motifs in the EMT network. a Empirical p value for enrichment of the number of positive feedback loops (PFL), Type-I motifs, Type-II motifs, or mutual-inhibition single-self-activation (MISSA) motifs. Strongly connected permutations of the strongly connected component were considered as the background for the “strongly connected” case; any permutations of the whole network were considered as the background for the “any” case. Above the dashed line, p < 0.05. b Cumulative density plots showing the proportion of permuted networks with respect to motif count cutoff. Vertical green lines show the actual EMT network’s motif counts. The empirical p value in a is one minus the cumulative density at the actual network’s count. Above the dashed line, cumulative density > 0.95, i.e. p < 0.05