Fig. 3

Detecting associations with HiCognition. a, b Visualization of regional heterogeneity and clustering with the Embedding widget for 34,857 SMC3 ChIP-seq peaks based on the ChIP-seq read densities of STAG1 and STAG2. a Cluster 1, representing SMC3 ChIP-seq peaks enriched in STAG1. b Cluster 2, representing SMC3 ChIP-seq peaks enriched in STAG2 ChIP-seq reads. c, d Analysis of common patterns and associations for clusters 1 and 2 as in a, b. c Average read density of STAG1 and STAG2 (i) and SMC3 (ii), average Hi-C contact map (iii), and LOLA analysis for associations with 11 region datasets. d analysis as in c for Cluster 2. e, f Validation of Lola analysis by ChIP-seq read density visualization. e Average ChIP-seq reads of Sororin and H3K4me1 for the STAG1-enriched cluster 1 as in Fig. a, c. f Average ChIP-seq reads of Sororin and H3K4me1 for the STAG2-enriched cluster 2 as in Fig. b, d