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Published online before print October 15, 2001, 10.1101/gr.184501
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Vol. 11, Issue 11, 1861-1870, November 2001

LETTER
Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500-Element cDNA Array

Judith M. Boer,1,5 Wolfgang K. Huber,1 Holger Sültmann,1 Friederike Wilmer,1 Anja von Heydebreck,2,6 Stefan Haas,1,2 Bernhard Korn,1,4 Bastian Gunawan,3 Andreas Vente,4 Laszlo Füzesi,3 Martin Vingron,2,6 and Annemarie Poustka1,7

Departments of 1 Molecular Genome Analysis and 2 Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany; 3 Institute of Pathology, Georg-August-Universität, Göttingen, Germany; 4 Resource Center Primary Database, Berlin/Heidelberg, Germany

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

[Expression data for the differentially expressed cDNAs are available as a Web supplement at http://www.dkfz-heidelberg.de/abt0840/whuber/rcc. The array data have been submitted to the GEO data repository under accession no. GSE3.]

Present addresses: 5Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands; 6Max-Planck-Institute for Molecular Genetics, Berlin, Germany.

7 Corresponding author.

11:1861-1870 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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