Figure 3

Unsupervised hierarchical clustering and lists of differentially expressed genes in FFPE. A. Heat map of hierarchical clustering. Normal breast tissue samples in FFPE (color coded and labeled at the top) and corresponding FF samples are shown in columns. Log₂ transformed signal intensities of 2820 differentially expressed genes are shown in color code (bar at bottom) in rows. B. Venn diagram showing overlap between the three lists of the differentially expressed genes (at FDR 0.05 level and at least 2-fold) in FFPE compared to FF samples from three different analyses - normal breast tissue only (bottom left showing 2820 genes), corresponding breast tumor tissue only (bottom right showing 1159 genes) and combined analysis of normal & tumor tissue (top center showing 1863 genes).