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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(15):2390-2398; doi:10.1093/bioinformatics/bth256
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.

GEPIS—quantitative gene expression profiling in normal and cancer tissues

Yan Zhang 1, David A. Eberhard 2, Gretchen D. Frantz 2, Patrick Dowd 4, Thomas D. Wu 1, Yan Zhou 1, Colin Watanabe 1, Shiuh-Ming Luoh 1, Paul Polakis 3, Kenneth J. Hillan 2, William I. Wood 1 and Zemin Zhang 1,*

1 Department of Bioinformatics, 2 Department of Pathology, 3 Department of Molecular Oncology and 4 Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA

Received on January 12, 2004; revised on March 1, 2004; accepted on March 2, 2004
Advance Access Publication April 8, 2004

Motivation: Expression profiling in diverse tissues is fundamental to understanding gene function as well as therapeutic target identification. The vast collection of expressed sequence tags (ESTs) and the associated tissue source information provides an attractive opportunity for studying gene expression.

Results: To facilitate EST-based expression analysis, we developed GEPIS (gene expression profiling in silico), a tool that integrates EST and tissue source information to compute gene expression patterns in a large panel of normal and tumor samples. We found EST-based expression patterns to be consistent with published papers as well as our own experimental results. We also built a GEPIS Regional Atlas that depicts expression characteristics of all genes in a selected genomic region. This program can be adapted for large-scale screening for genes with desirable expression patterns, as illustrated by our large-scale mining for tissue- and tumor-specific genes.

Availability: The email server version of the GEPIS application is freely available at http://share.gene.com/share/gepis. An interactive version of GEPIS will soon be freely available at http://www.cgl.ucsf.edu/Research/genentech/gepis/. The source code, modules, data and gene lists can be downloaded at http://share.gene.com/share/gepis

Supplementary information: Supplementary tables and figures are available at http://www.cgl.ucsf.edu/Research/genentech/gepis/

Contact: zemin{at}gene.com

* To whom correspondence should be addressed.


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