Figure 2. Correlation between gene expression and genome alterations on the 6q regions.

Genomic and gene expression profiles were established for 188 breast tumors (32 luminal B and 156 non luminal B identified at the top by blue and grey boxes, respectively) in three 6q regions: 6q14.1-q22.31 (top), 6q22.31-q23.1 (middle) and 6q23.2-q24.2 (bottom). For each region, heatmaps for genome copy number and gene expression profiles are consecutively drawn. Genome copy number was measured by aCGH on probes or groups of probes spanning each of these regions. Red indicates increased copy number and green indicates decreased copy number. In the heatmap tumors are organized from the tumor that presented the most copy number losses to the tumor that exhibited the most copy number gains. The next heatmap was established with the expression of the independent genes located on the corresponding 6q region and profiled in the same 188 tumors similarly organized. For gene copy number and gene expression heatmaps, we used color scale limits from −3 to +3 and −2 to +2, respectively. Next to the right, are plotted genes successively selected by steps I, II and III of the integrated analysis “aCGH & mRNA expression” as defined by the work pipeline (Figure S2). Grey and green lines correspond to rejected and selected genes, respectively. Among genes with an expression level that varied according to CNAs, we retained genes showed significant differences (vertical line) in copy number loss correlated with downregulated expression in luminal B compared to non-luminal B tumors. They were qualified as potential TSGs. For each region, only the first five most significant are listed. PNRC1, NCOA7 and TNFAIP3 genes were the most significant candidate TSGs for the 6q14.1-q22.31 (top), 6q22.31-q23.1 (middle) and 6q23.2-q24.2 (bottom) regions, respectively.