Enrichment analysis of GO functions and KEGG pathways revealed that these DEGs were significantly enriched (FDR <0.05) in regulations of chromatin organization, protein phosphorylation, RNA polymerase II transcription, and signaling pathways of breast cancer, EGFR and Notch (Figures 5B,C and Supplementary Table S5), such as up-regulated EZH2, JRKL and KLF3 with gained EPIs and down-regulated FOXA1, FA2H and MAPK13 with lost EPIs (Figures 5C–E, Supplementary Figure S6). This evidence concerns the gene KLF3 and breast carcinoma.