Fig. 3

Properties of RER regions and tumor subtypes. a Unsupervised hierarchical cluster analysis of breast tumor samples for RER regions at 3p14-p21.31 (left) and 16q12.2-q24.1 (right). Heat maps of gene expression z scores with hierarchical clustering of samples (red high expression, green low expression). Genes are ordered by their position in the genome. Subtype information [22] for each tumor sample is identified by the color-coded matrix: luminal A (blue), luminal B (turquoise), ERBB2 (purple), basal (red), normal-like (green). Only genes in the regions with significant TCSs are shown. b As in (a) but for mean expression (mean z score of genes with significant TCSs) for all RER regions in each breast tumor sample, showing clustering of RER regions into three groups. Both the RER regions and samples were subject to hierarchical clustering. c Box plots showing mean expression (mean z score of genes with significant TCSs) of RER regions from clusters 1, 2 and 3 in breast tumors of different subtypes; luminal A (LumA, blue), luminal B (LumB, turquoise), ERBB2 (purple), basal-like (red). **p < 0.01, ***p < 0.001, Wilcoxon test)