CMTC gene expression pattern, prognostic framework, and oncogenic pathway activity. (A) The 803-gene signature (represented by 828 oligonucleotide probes) was used to classify the gene expression pattern in the 149 breast cancers in the training cohort into the three main clusters of CMTC. Tumors in CMTC-3 were mostly Her2+/TN as well as CMTC-1 and CMTC-2 non-Her2+/TN. The bottom multicolor bars indicating Her2+/TN are as follows: Her2+, deep pink; TN, dark blue. The multicolor bars indicating grade are as follows: grade 1, dark blue; grade 2, dark orange; and grade 3, deep pink. The multicolor bars indicating subtype and PAM50 are as follows: normal-like, lime; luminal A, blue; luminal B, dark orange; basal-like, dark blue; and Her2+, deep pink. CMTC = ClinicoMolecular Triad Classification; Her2 = human epidermal growth factor receptor 2; TN = triple-negative; ER2+ = estrogen receptor-positive; TGFβRII = transforming growth factor β receptor type II. (B) The probabilities of pathway activation of 19 published oncogenic pathway signatures in the 149 breast cancers in the training cohort. Blue indicates low pathway activity, and red indicates high activity. EGFR = epidermal growth factor receptor; PAM50 = 50-gene prediction analysis of microarray; PI3K = phosphatidylinositol 3-kinase; PR = progesterone receptor; STAT3 = signal transducer and activator of transcription 3.