Figure 2
Expression levels of gene signatures in breast cancer tumors. (A) The means of the log2 expression levels of the genes in each signature were calculated for 982 breast cancers by using data from The Cancer Genome Atlas project. The tumors were subjected to non-supervised hierarchical clustering based on the signatures. Subtypes, determined by PAM50 centroids, are indicated in color. (B) The mean log2 expression levels of the genes in the signatures with the largest number of genes representing (ECM) genes (signature 1), endothelial genes (signature 4), and immune/inflammatory genes (signature 6) are shown for the indicated breast cancer subgroups. Asterisk indicates that the value is lower than in the groups without asterisk; P <10−7 (analysis of variance followed by Tukey’s honest significance test) except signature 4 (HER2 versus luminal A, P = 0.0016) and for signature 6 (luminal A versus HER2, P = 0.030; luminal B versus HER2, P = 0.000018; and luminal B versus normal, P = 0.0000062).