pairs of states across the 43 epigenomes. In order to differentiate between chromatin state dynamics across tissues (inter-tissue) relative to variation of states across individuals or replicates from the same tissue (intra-tissue), we also computed analogous switching frequencies by restricting to subgroups of epigenomes from the same tissue type (Table S1 - Sheet VariationAnalysis). The frequencies were added across all sub-groups and then row normalized to switching probabilities. Fig. S7a. shows the intra-tissue switching probabilities. We then computed the relative enrichment of state switches as the log10 ratio of inter-tissue switching probability across the 43 epigenomes relative to the intra-tissue switching probabilities (Fig. 5c). We repeated this analysis on the 16 ENCODE cell-lines and obtained similar conclusions regarding relative enrichment of state switches (Fig. S7c). Analogous analyses were performed using the 18-state expanded model in Roadmap Epigenomics samples (Extended Data 5c) and ENCODE samples (Fig. S7d).
