Second, we apply it to estimate activation levels of modules within a number of important molecular pathways (HRAS, E2F3, MYC, ERBB2, EGFR, AKT, IL12, IL2, IL4, IL13, IFNG, TGFB) (Methods) [1,3,11,25,38,39] in ER+ and ER- breast cancer and show that specific pathway modules synergize to provide better prognostic stratifications of tumour samples. This evidence concerns the gene E2F3 and breast carcinoma.