Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array

We investigated the changes in gene expression accompanying the development and progression of kidney cancer by use of 31,500-element complementary DN A arrays. We measured expression profiles for paired neoplastic and noncanc erous renal epithelium samples from 37 individuals. Using an experimental d esign optimized for factoring out technological and biological noise, and a n adapted statistical test, we found 1738 differentially expressed cDNAs wi th an expected number of six false positives. Functional annotation of thes e genes provided views of the changes in the activities of specific biologi cal pathways in renal cancer. Cell adhesion, signal transduction, and nucle otide metabolism were among the biological processes with a large proportio n of genes overexpressed in renal cell carcinoma. Down-regulated pathways i n the kidney tumor cells included small molecule transport, ion homeostasis , and oxygen and radical metabolism. Our expression profiling data uncovere d gene expression changes shared with other epithelial tumors, as well as a unique signature for renal cell carcinoma.