D842 Nucleic Acids Research, 2009, Vol. 37, Database issue and mechanistic information about gene-behavior relation- ships. Thus, we searched orthologs of the ethanol-related genes in this database. For the nonhuman genes in our datasets, their human ortholog information was obtained and curated. We obtained human/mouse and human/rat ortholog information from MGI (ftp://ftp.informatics. jax.org/pub/reports/index.html), and human/ﬂy and human/worm from the Inparanoid database (version 6.1, http://inparanoid.sbc.su.se/download/6.1/) (25). DATABASE CONTENT AND ORGANIZATION Data overview As summarized in Table 1, we have collected and curated more than 30 genome-wide or large-scale datasets includ- ing microarray gene expression, linkage and genome-wide association studies, results of literature search and 21 mouse QTLs. At present, ERGR includes 7000 genes in ﬁve organisms: human (3311), mouse (2129), rat (679), ﬂy (614) and worm (228). For rat, ﬂy and worm, ERGR only has microarray expression data. Because of the major research interest in humans, the human data in ERGR is the most comprehensive, which includes micro- array gene expression, linkage studies, genome-wide asso- ciation study and literature search results. Database organization We used MySQL, a SQL client/sever relational open source database management system that has been com- monly used in the development of biomedical databases, to store and manage the data. One table was speciﬁ- cally designed to store the summary descriptions of all datasets. Because the formats of the datasets generated by the diﬀerent methods often varied, we managed data- sets of gene expression, linkage, association or QTLs by separate tables. Annotations of gene information, gene ontology, reference sequences and ortholog information were also stored in individual tables. Dataset name, PubMed ID and Entrez gene ID are the keys to link between tables. Table 1. Summary of the data in ERGR Species Human (Total: 3311 genes) Method Microarray expression Genome-wide association Linkage HuGE Navigator Addiction array list Literature search Microarray expression QTL Microarray expression Microarray expression Microarray expression Mouse (Total: 2129 genes) Rat Fly Worm WEB INTERFACE A user-friendly web interface was designed and implemen- ted for ERGR. It is freely available at http://bioinfo. vipbg.vcu.edu/ERGR/. The user can browse and search all the data at diﬀerent levels or combine the data by the integration functions. Data browse To help the user to browse the data easily, ERGR provides four diﬀerent browsing methods: (i) by species; (ii) by method or platform such as microarray expression, linkage or association; (iii) by chromosome of a species; (iv) or through a summary page which lists all the datasets available in ERGR. A cascading style is applied for data- set browse, i.e., from dataset list to gene list, and then to gene information. By clicking the dataset name on a data- set list page it will show the dataset description and the corresponding list of genes. Selecting the gene ID will link to the gene information page, which includes gene ID, symbol and name, GO annotation, RefSeq, chromosome location, database cross links and the detailed study information (e.g. fold change of gene expression and P-value) extracted from the original ethanol studies. For example, based on the microarray dataset ‘15816859’, the fold change and P-value of ADH6 gene expression were 0.69 and 7.00 10 3, respectively (http://bioinfo.vipbg. vcu.edu/ERGR/geneinfo.php?id=130). Moreover, the user may ﬁnd the detailed information of the studied single nucleotide polymorphisms (SNPs) via dynamic links to the NCBI dbSNP database. Data search ERGR provides three approaches for searching the data including text search and sequence search. First, the user may ﬁnd a quick search box in the top right of the web page for searching gene ID and symbol. It supports wild- card searches such as using partial gene symbol (e.g. ADH) or using an asterisk (e.g. ADH ). Second, ERGR provides an advanced search page, on which users may combine diﬀerent search terms (e.g. ID, symbol, phenotype, physical location and GO term) for a user-deﬁned search. Literature Literature Literature HuGE Navigator (http://www.hugenavigator.net/) Literature Literature Literature PARC Alcohol QTLs (http://www.ohsu.edu/ parc/by_phen.shtml) Literature Literature Literature No. of datasets No. of genes Source 7 1 3 9 diseases 1 1 11 21 QTLs 6 2 1 831 71 918 203 130 1726 682 1568 679 614 228