Overlap between module genes and established signatures.

Modules 1-ER, 11-Prolif, 7-ERBB2 and 2-Dev/Basal share genes in common with the PAM50 gene set used to evaluate intrinsic subtype, the NKI70 prognostic classifer used in MammaPrint, or the 21-gene prognostic signature used in OncotypeDX. Immune modules 3–5, histone module 6-Hist, the stromal modules 8 and 9-ECM/Dev/Immune, and the ECM module 10-ECM have no genes in common with these signatures. Listed genes are present in both the specified module and the labeled signature. Genes in bold face are present in the module and multiple signatures.