Fig. 3: Differentially activated enhancers in human CRC.

a Unsupervised clustering analysis and Pearson correlation heatmap of H3K27ac ChIP-seq data for the 33,131 ChromHMM-defined active enhancers clearly distinguish patient-derived organoids (PDOs) from normal colon tissues. b Volcano plot of differentially enriched enhancer regions between PDOs and normal colon mucosa. Dotted lines indicate thresholds for two-sided adjusted P-value < 0.01 and |log2 fold-change > 2 (Wald test with Benjamini–Hochberg false discovery rate correction). c Percentage of gained enhancers shared by different PDOs (see Supplementary Fig. 4b, c). d–e Representative tracks of H3K27ac and ChromHMM profiles, illustrating examples of gained (d) and lost (e) enhancer regions in PDOs compared to normal colon mucosa. Shaded boxes indicate the presence or absence of H3K27ac peaks. Interactions between gained enhancers and promoter regions based on chromosome conformation capture (capture Hi-C) data on human colon cancer²² are shown below the graph. f The Hippo signaling pathway is the most significantly enriched pathway related to the gained enhancer-associated genes that are upregulated in PDOs compared to normal tissues. The size of the circles corresponds to the number of gained-enhancer associated genes present in the geneset of a particular KEGG pathway (Gene Ratio). The dotted line indicates the threshold for significantly enriched pathways based on a two-sided Fisher’s exact test with a false discovery rate (FDR) < 0.05. g Visualization of pathway network for tumor-upregulated genes annotated to gained enhancers based on functional enrichment analysis. Pathway terms are represented by circles, the size of which is proportional to the number of genes. The circles are colored according to the enrichment P-value based on a two-sided Fisher’s exact test.