Identification of the claudin-low subtype in a panel of breast cancer cell lines. Gene clusters that characterize each primary human tumor subtype are shown in the human and cell line gene expression data sets. In both data sets, array trees have been derived by unsupervised hierarchical clustering using the intrinsic list from Parker et al.  as shown in Figure S1A and S4A in Additional file 1. (a) The top 50 upregulated genes associated with each molecular subtype, including the top 50 downregulated genes in claudin-low tumors, are shown in the UNC337 database. Top genes were selected after performing a two-class SAM (FDR = 0%) between each molecular subtype versus others. Luminal A and B subtypes were combined into the luminal subtype. In the tree, the yellow node denotes the claudin-low tumors defined by SigClust . (b) Gene clusters characteristic of each tumor molecular subtype are shown in 52 breast cancer cell lines from Neve et al. . Missing genes have been omitted. In the tree, the yellow node denotes the most highly correlated cell lines that best resemble the claudin-low subtype. 1 (yellow), claudin-low gene cluster of upregulated and downregulated genes; 2 (red), basal-like gene cluster; 3 (pink), HER2-enriched gene cluster; 4 (green), normal breast-like gene cluster; 5 (blue), luminal gene cluster.