Co-clustering of real-time quantitative reverse-transcription (qRT)-PCR and microarray data using 50 genes and 252 samples. The relative copy number (qRT-PCR) and R/G ratio (microarray) for each gene was log2-transformed and combined into a single dataset using distance-weighted discrimination. Two-way hierarchical clustering was performed on the combined dataset using Spearman correlation and average linkage. (a) The sample-associated dendrogram shows the same classes as seen in Figure 1. Samples are classified as Basal-like (red), HER2+/ER- (pink), Luminal (blue), and Normal-like (green). The expression level for each gene is shown relative to the median expression of that gene across all the samples, with overexpressed genes in red and underexpressed genes in green. Genes with average expression are black. (b) The gene-associated dendrogram shows that the Luminal tumors and Basal-like tumors differentially express estrogen-associated genes (cluster 1); as well as basal keratins (KRT 5 and KRT 17), inflammatory response genes (CX3CL1 and SLPI), and genes in the Wnt pathway (FZD7) (cluster 3). The main distinguishers of the HER2+/ER- group are low expression of genes in cluster 1 and high expression of genes on the 17q12 amplicon (ERBB2 and GRB7) (cluster 4). The proliferation genes (cluster 2) have high expression in the estrogen receptor (ER)-negative tumors (Basal-like and HER2+/ER-) and low expression in ER-positive (Luminal) and Normal-like samples.