W152–W158 Nucleic Acids Research, 2007, Vol. 35, Web Server issue doi:10.1093/nar/gkm381 GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database 1 1 1 2 Yan Zhang , Shiuh-Ming Luoh , Lawrence S. Hon , Robert Baertsch , 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 Received January 31, 2007; Revised April 27, 2007; Accepted April 30, 2007 ABSTRACT 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/. INTRODUCTION Analysis of gene expression proﬁles across various tissue types is essential for understanding gene functions. Among various available expression data sources, expressed sequence tags (ESTs) have been valuable for rapid expression proﬁling. Based on the premise that EST clone frequency is proportional to the corresponding gene’s expression level (1), we and others have developed algorithms and tools to perform expression analysis based on EST data (2–7). Meanwhile, EST data continue to accumulate at a rapid pace, and there are a growing number of databases that organize general or species- speciﬁc EST information, including EST data for sea bass, wheat, chicken, pig and tomato (8–12). Despite the surge of recent progress in other species, the number of public EST entries for human and mouse still far exceed those for any other species, based on the January 2007 summary from dbEST (http://www.ncbi.nlm.nih.gov/ dbEST/). Since the reliability of EST-based expression analysis is dependent on the size of EST libraries, the human and mouse data remain an attractive source for expression analysis, and the tools built for analyzing these data will likely beneﬁt expression analysis for other species. We previously developed the GEPIS server that utilizes EST abundance information to calculate gene expression levels in a panel of normal and cancerous human tissues for a given input DNA sequence (7). We showed that such EST-based (or ‘digitally’ derived) expression units exhibit a linear correlation with TaqMan-determined expression levels. Since its release, the GEPIS server has provided expression results for over 30 000 requests by researchers from 460 countries. Despite its usefulness, GEPIS suﬀers from several limitations. The method relied on the BLAST program to assign EST sequences to a given input mRNA sequence. However, BLAST often erroneously links ESTs to input sequences due to high-percentage regional matches. As a result, a given EST could be matched to multiple genes, thus leading to miscalculated expression data. In addition, there were insuﬃcient data for performing reliable analysis for mouse genes. The design of the system also did not allow easy development of new functionality commonly requested by users, such as URL linking to the expression results, text searching and display of detailed results. *To whom correspondence should be addressed. Tel: þ1 650 225 4293; Fax: 650 225 5389; Email: zemin@gene.com 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.