Fig. 4: EpiVerse enables the analysis of whole human chromatin structure.

a Hi-C-based dendrogram: A dendrogram illustrating hierarchical clustering of 39 different tissue types based on similarities in their Hi-C features, revealing potential functional or developmental relationships. b Boxplot of Hi-C value quantile and active enhancer counts: Boxplot compares the distribution of Hi-C interaction values across four quantiles to the counts of active enhancers (n = 11,152; data divided into quartiles), highlighting a trend that suggests a relationship between chromatin interaction frequency and enhancer activity. The two-sided Mann–Whitney test was conducted, with significance indicated by asterisks: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. Pairwise comparisons between groups for three tissues: H1 (0 vs. 1, \({{\rm{p}}}=2.068\times {10}^{-255}\); 1 vs. 2, \({{\rm{p}}}=9.135\times {10}^{-112}\); 2 vs. 3, \({{\rm{p}}}=3.487\times {10}^{-176}\); 0 vs. 3, p = 0), brain (0 vs. 1, \({{\rm{p}}}=5.679\times {10}^{-165}\); 1 vs. 2, \({{\rm{p}}}=4.01\times {10}^{-89}\); 2 vs. 3, \({{\rm{p}}}=7.845\times {10}^{-168}\); 0 vs. 3, p = 0), pancreas (0 vs. 1, \({{\rm{p}}}=3.641\times {10}^{-225}\); 1 vs. 2, \({{\rm{p}}}=4.224\times {10}^{-180}\); 2 vs. 3, \({{\rm{p}}}=4.968\times {10}^{-251}\); 0 vs. 3, p = 0). Boxplot elements are defined as follows: center line represents the median; box limits indicate the upper and lower quartiles; whiskers extend to 1.5 times the interquartile range from the quartiles; and points denote outliers. c Promoter hubness in tissue-specific genes across six tissues: A visual representation of promoter hubness, which reflects the number of connections a promoter has, across six different tissues, showing its correlation with the expression of tissue-specific genes. d GO term analysis of genes in regions with the largest Hi-C contact variation: GO term analysis of genes located in regions with the largest variation in chromatin structure highlights strong tissue specificity. This figure demonstrates the critical role of chromatin organization in defining tissue- and cell-specific functions, with significant enrichment in skin, tonsil, breast, tongue, bronchial epithelial cells, colon, and normal human epidermal keratinocytes (NHEK).