For each cancer type, patient samples were first classified by unsupervised clustering based on the signature TFAs then annotated with their associated pathological grades or PTEN status, determined by either CGH analysis for PTEN copy number (CN) alterations in prostate cancers [35] or immunohistochemistry (IHC) and mRNA array for PTEN expression in breast cancers [32]. The gene discussed is PTEN; the disease is breast cancer.