Fig. 4

Co-enriched genomic elements identified using ACT2 exhibit distinct gene expression profiles. A–D Violin plots depicting expression profiles of gene sets in the indicated categories. p-values were obtained using Wilcoxon rank sum tests. A Violin plot depicting the expression profiles of genes that exhibited (co-)enrichment of H3K4me3 and/or H3K27ac at the gene promoter. Gene expression was calculated as reads per kilobase mapped (RPKM). Using a significance threshold of α < 0.005, the null hypothesis of no difference in the gene expression profile of co-occupied promoters was rejected. B Violin plot as in panel A but using enrichment status at gene enhancers. Enhancers were defined as regions enriched for H3K27ac, and thus the H3K4me3-alone category was not included. Gene expression values were matched to enhancers based on proximity. Using a significance threshold of α < 0.005, the null hypothesis of no difference in the gene expression profile of co-occupied enhancers was not rejected. C Violin plot depicting the expression profiles of genes that exhibited (co-)enrichment of H3K4me3 and/or H3K9me3 at the gene promoter. Gene expression was calculated as reads per kilobase mapped (RPKM). Using a significance threshold of α < 0.005, the null hypothesis of no difference in the gene expression profile of co-occupied promoters was rejected. D Violin plot as in panel C but using ENCODE ChIP-seq data. Since co-occupancy cannot be examined in these data, the presence of overlapping H3K4me3 and H3K9me3 peaks within the promoter regions was used as a proxy. Using a significance threshold of α < 0.005, the null hypothesis of no difference in the gene expression profile of promoters containing overlapping expression peaks was rejected. E Scatter plot examining the correlation between H3K9me3 and H3K4me3 read densities across the genome. Each data point represents a genomic fragment of five kilobases in length. Fragments exhibiting only H3K9me3 enrichment with no detectable H3K4me3 enrichment are depicted in red on the y-axis. F Violin plot depicting the expression profiles of genes that exhibited enrichment of H3K9me3 but not H3K4me3 at the transcription start site (TSS) vs. all other genes. Gene expression was calculated as reads per kilobase mapped (RPKM). Using a significance threshold of α < 0.005, the null hypothesis of no difference in the gene expression profile of these genes vs. all other genes was rejected