By applying a context-specific network built from the TCGA prostate cancer dataset, we could predict functional co-localization of FOXA1 and AR in target genes’ promoters after dihydrotestosterone (DHT) treatment in prostate cell lines (Additional file 1: Figure S22 and Fig. 5b), validating the known role of FOXA1 in AR-regulated gene transcription in prostate cancer [25, 26]. Here, AR is linked to prostate carcinoma.