Validation of genes selected by FADA from the Welsh et al. dataset  as overexpressed in prostate cancer. (A) RT-PCR was applied to 14 paired prostate tumor – normal prostate samples to determine the expression levels of a selection of genes shown by FADA as significantly overrepresented in prostate cancer (HPN, KLK3, IQGAP2, POR1 and HER3), and additional genes relevant to this tumor (genes for the receptor tyrosine kinases EGFR, HER2, HER4, and genes for the steroid hormone receptors AR, ERα and ERβ). The expression values for each gene, previously normalized with respect to the S14r expression level in each sample, are shown as ratios of the normalized values in prostate cancer vs. values in the matching normal prostate tissue. Quantitation of desmin expression levels was used to assess the degree of contribution of stromal components in the samples analyzed. Values equal to or above 100-fold are shown as 100. (B) Heatmap representation of the same data (color scale as shown below). (C) Real-time PCR analysis for HER3 transcript levels of laser microdissected tumor and normal samples, compared with relative transcript levels in enriched (non-microdissected) tissues from the same cases. (D) Immunohistochemical analysis of HER3 on paraffin-embedded prostate tissue sections arranged in tissue microarrays (see Methods). Left, low magnification image (×100) of one case, with weak staining for HER3 in normal glands (n), and a strong staining in tumor epithelial cells (t). Right, higher magnification (×400) of a second case.