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Nucleic Acids Research Advance Access published online on June 1, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm381
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database

Yan Zhang1, Shiuh-Ming Luoh1, Lawrence S. Hon1, Robert Baertsch2, William I. Wood1 and Zemin Zhang1,*

1Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and 2Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA

*To whom correspondence should be addressed. Tel: +1 650 225 4293; Fax: 650 225 5389; Email: zemin{at}gene.com

Received January 31, 2007. Revised April 27, 2007. Accepted April 30, 2007.

GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from mRNA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis and linking between mouse and human genes. GeneHub-GEPIS is available at http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ or http://www.gepis.org/.


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