Fig. 3
Prediction of non-classical functions in ChIP-seq data-rich cell types. a Top 10 ranked non-classical functions and the corresponding cofactor candidates of HMRs. Non-classical functions of HMRs are ranked by adjusted R2 of the cofactor. For non-classical functions candidates from multiple ChIP-seq data of the same HMR, the top ranked non-classical function candidates are kept. For each non-classical function candidate, the top 5 cofactor candidates are showed. The previously reported non-classical functions are highlighted in red. b Heatmap showing EZH2, H3K27me3, E2F1, and H3K4me3 enrichment around EZH2 ChIP-seq peak centers. Rows represent EZH2 binding sites and are ranked by the normalized H3K27me3 signals at EZH2 binding sites. The colors indicate the normalized ChIP-seq enrichment level and the values are scaled by row. EZH2, E2F1, H3K27me3, and H3K4me3 ChIP-seq data in mESCs were obtained from GSE49431, GSE11431, GSE58023, and GSE73432. c Venn diagram showing the significant overlap of target promoters (±3 kb around TSSs of genes) between EZH2 non-classical sites cobound by E2F1 in mESCs and converted EZH2 non-classical sites cobound by E2F1 from human abl cell line. Fisher’s exact test was performed to identify statistical significance. The dot plot shows that target genes of overlap sites were enriched in biological processes such as mRNA processing. Gene ontology analysis of target genes was performed using the R package clusterProfiler [34]. Top 7 significant (Benjamini-Hochberg-adjusted p value < 0.01) terms are shown. d Heatmap showing RNF2, H2Aub1, MED12, and KDM1A enrichment around RNF2 ChIP-seq peak centers. Rows represent RNF2 binding sites and are ranked by the normalized H2Aub1 signals at RNF2 binding sites. The colors indicate the normalized ChIP-seq enrichment level and the values are scaled by row. RNF2, MED12, KDM1A, and H2Aub1 ChIP-seq data were obtained from GSE55697, GSE22557, GSE27841, and GSE34518. e Venn diagram showing the significant overlap between non-classical RNF2 sites cobound by MED12 and sites cobound by KDM1A. Fisher’s exact test was performed to identify statistical significance