A module associated with NF1 shallow deletion contained several genes that are considerably important in both ER + breast cancers and endocrine resistance, including ESR1 and FOXA1. Unsupervised hierarchical clustering revealed that breast cancers with NF1 shallow deletions form a distinct cluster that correlate with estrogen receptor (ER)-negative breast cancer and RAS activation. Here, FOXA1 is linked to breast carcinoma.