Nucleic Acids Research, 2007, Vol. 35, Web Server issue W155 of input record. The text search is case-insensitive and a begin-search is automatically performed if no exact match is found. All of the source code is available upon request. PROGRAM DESCRIPTION GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues. The design of the system is depicted in Figure 1. The application is composed of two parts: a front-end web interface for user input, data retrieval, display and download, and a backend engine to perform GeneHub-GEPIS analysis and data storage. The backend expression analysis relies on an integrated gene database we constructed that stores gene deﬁnitions and cross-references. Much of the documentation of this application is provided in the form of FAQs so that answers to commonly asked questions are provided on the spot. Data input GeneHub-GEPIS supports both text- and cDNA sequence-based data retrieval (Figure 2). For text, the application allows diverse input values ranging from gene symbols to various accession identiﬁers. It currently supports identiﬁers from common gene databases (GenBank, RefSeq, Ensembl, FANTOM, Entrez Gene, UniGene, miRBase), protein databases (PDB, UniProt) and commercial microarray platforms (Aﬀymetrix and Agilent). For sequence-based retrieval users can either upload a single-sequence FASTA ﬁle to the web server or paste a nucleotide sequence in a text box. Users can also search for either human or mouse genes regardless the origin species of the input text and sequences. If the target species is diﬀerent from the species of the input value, an ortholog search is automatically performed. The applica- tion also allows users to limit their search to a speciﬁed chromosome to avoid possible multiple matches to the input text. It is worth noting that GeneHub-GEPIS allow direct URL access from any web pages, with a gene symbol or accession as argument. For example, when retrieving mouse c-Met results, the URL is: http://www.cgl. ucsf.edu/cgi-bin/genentech/genehub-gepis/web_search.pl? intype¼1&xreﬁd¼cMet&species¼mouse. To obtain results for RefSeq identiﬁer NM_001260 (human ERBB2), the URL is: http://www.cgl.ucsf.edu/cgi-bin/ genentech/genehub-gepis/web_search.pl?intype¼1&xreﬁd ¼NM_001260&species¼human. Using this feature, some of the gene-based web servers, such as the widely accessed UCSC Known Genes web pages, have created links to GeneHub-GEPIS results. This is important as it can greatly increase the use of this server. Program output Once a unique gene match is found as one of the pre- deﬁned GeneHub genes, the program directly retrieves the pre-computed EST-based gene expression results. The initial result page provides navigation links to download the result, display EST hits by libraries, and view additional graphic charts. Expression data is displayed in both a tabular format and a graphic chart (Figure 3A). The program also retrieves and displays information about input genes such as gene names, synonyms, description, genomic locations and provides links to the UCSC genome browser and others web resources such as GEO microarray results (Figure 3B). Since it is often desirable to examine the expression pattern of an orthologous gene, we provide links that allow user to quickly navigate between the result pages of human and mouse ortholog pairs. In addition, users can specify a genomic region and tissues of interest to get a Regional GEPIS Atlas view, which displays the expression values of all of the neighbor genes (Supplementary Figure 2). We also implemented a frequently requested feature that displays library information and the number of EST hits Figure 1. Conceptual representation of the design of the GeneHub-GEPIS application.