Fig. 9

Multi-omics data integration reveals single and combinatorial chromatin remodeling events that affect gene transcription and cell phenotype. a ChromHMM segmentation of the genome. TES: Transcription end site, S: States 1–15. Integration of ChromHMM with b RNA-seq, c DNA methylation, and d ATAC-seq. Chromatin segmentation of e two upregulated genes, Btc and Etv5 and f two downregulated genes, Acta2 and Pdgfrb illustrating the change in marks at 0 and 24 hrs. g Heatmap displaying log2 fold changes of genes in the RNA-seq, ATAC-seq, ChIP-seq, and methylation ratio of RRBS data set at 24 hrs. h Pathway enrichment analysis of genes represented in panel g using RITAN. Gain or loss of enrichment: RNA-seq genes enriched in (1) ATAC-seq (2), H3K27ac (3), H3K4me3 (4), H3K4me1 (5), H3K36me3 (6), H3K27me3 (7), H3K9me3, and (8) hypermethylated (gain), hypomethylated (loss) gene promoters respectively. i Gene networks generated from the genes represented in g. Center red or blue dots represent upregulated and downregulated genes in the RNA-seq data set respectively. Concentric circles around the dots represent changes in H3K27ac, H3K4me3, and H3K36me3 respectively (going inside out) with red representing gain of the mark and blue representing loss of the mark.  Enlarged figure with gene details provided as Additional file 1: Fig S10. j RPKM expression levels of differentially expressed histone readers, writers, and erasers normalized to the Z scale and plotted for 0, 12, 24, and 48 hrs