Based on differential methylation analysis and correlation with RNAseq data, we identified that FOXA1, a key transcription factor essential for ER and AR attachment to chromatin and the subsequent transcriptional induction of luminal genes in breast cancer cells (see ref. 42 for a review), shows a strikingly selective correlated pattern between specific hypermethylation in the CpG dense promoter region and mRNA downregulation in Basal-like breast cancer, irrespective of ER, PR, and HER2 status. The gene discussed is ESR1; the disease is breast carcinoma.