HOXA11 and breast cancer: Genes more highly methylated in HR+, luminal, or p53 wild-type breast cancers included FABP3, FGF2, FZD9, GAS7, HDAC9, HOXA11, MME, PAX6, POMC, PTGS2, RASSF1, RBP1, and SCGB3A1; among the genes more highly methylated in HR-, basal-like, or p53 mutant tumors were BCR, C4B, CDH17, DAB2IP, MEST, RARA, SEPT5, SERPINA5, TFF1, and THY1. Among the p53-related genes, 34 were also associated with p53 mutation status in the study of Ronneberg et al.[37] (Additional file 8: Figure S2B).