Fig. 3

Super-enhancer in tumor involved in breast cancer tumorigenesis. a Distribution of H3K27ac ChIP-seq signal (normalize by ratio to highest H3K27ac reads number of enhancer) across the 14,352 tumor enhancers. b Metagene analysis of mean H3K27ac ChIP-seq density across 661 super-enhancers and 13,691 typical enhancers. Metagene plot is centered on the enhancer region. The number and mean size of super and typical enhancers are shown. c Box plot of average expression of genes (FPKM) adjacent to tumor typical enhancers and super-enhancers, and genes without enhancer, in normal and tumor tissues. d Matchstick plot showing the top 20 KEGG pathway associated with tumor super-enhancer-adjacent genes. e Pie plot showing the gene number of the three tumor super-enhancers adjacent gene clusters, which are increased in tumor, decreased in tumor, and no change in tumor compared to normal tissue. f UCSC browser view showing the ChIP-seq density of H3K27ac, H4K8ac, and RNA-seq signal in both normal tissue and tumor located in Xbp1 and Pak4 gene locus. g Venn diagram showing the gene number of the three different clusters indicated in the bottom. h Box plot of expression (FPKM) from super-enhancer adjacent genes of the three clusters illustrated in Fig. 3g. i Matchstick plots showing the top KEGG pathway terms of the three gene clusters identified in Fig. 3g