FOXA1 and breast cancer: After peak calling using peakzilla [35] and filtering out false-positive peaks due to genomic amplification in the HCC1954 breast cancer cells, we obtained 13,753 and 14,257 peaks for FOXA1 replicates samples and 2095 and 3751 peaks for GATA3 replicates samples (see examples in Fig. 4c,d and Additional file 1: Table S4).