Figure 2. Microarray Data.

(A) Hierarchical clustering based on the 990 most varying genes in 37 tumors with Affymetrix-grade RNA. C1, C2, and C3 denote the three tumor clusters. Annotations: TP53 status (red, mutant; yellow, wild-type); ESR1 (immunohistochemistry) (blue, positive; green, negative); basal cytokeratins (KRT5/6 or 17, immunohistochemistry) (orange, positive; gray, negative); ERBB2 (RT-PCR) (pink, positive; gray, negative); complete pathological response to chemotherapy (blue, complete; red, incomplete); and tumor grade (green, grade 3; purple, grade 1 or 2). For chemotherapy response, patients treated with other regimens are indicated by a question mark. P1, P2, etc. refer to the patient's references in Table S1.

(B) Genes linked to TP53 status (t-tests): the top and bottom genes (classified by fold changes [FC]) are shown.