Fig. 5

Integration of RNA-seq and ChIP-seq data in RMS cells treated with a combination of 2.5 µM ATRA and 5 µM GSK343 compared to DMSO control. A Volcano plot of genes involved in myogenesis in RD cells after treatment. B Gene ontology analysis of processes that are differentially regulated in RD cells treated with combination of 2.5 µM ATRA and 5 µM GSK343. C GSEA shows positive enrichment of myogenesis genes in RD after combination treatment. D Volcano plot of genes involved in the interferon α response pathway in RH30 cells after treatment. E Gene ontology analysis of processes that are differentially regulated in RH30 cells treated with combination of 2.5 µM ATRA and 5 µM GSK343. F GSEA shows positive enrichment of genes involved in the interferon α response in RH30 after combination treatment. Venn diagram showing the overlap of number of DEGs with EZH2 and RARα peaks identified from ChIP-seq in G RD and H RH30 cells