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      GeneCards Version 3: the human gene integrator

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          Abstract

          GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73 000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards’ unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations, and finds set-shared annotations by descriptor enrichment analysis. Such set-centric features address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting. We highlight the new Version 3 database architecture, its multi-faceted search engine, and its semi-automated quality assurance system. Data enhancements include an expanded visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways sections. GeneCards now provides direct links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs and features gene-related drugs and compounds lists. We also portray the GeneCards Inferred Functionality Score annotation landscape tool for scoring a gene’s functional information status. Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite.

          Database URL: www.genecards.org

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          Most cited references14

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          Gene Ontology: tool for the unification of biology

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            GeneCards: integrating information about genes, proteins and diseases.

            M Rebhan (1997)
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              The Mouse Genome Database (MGD): mouse biology and model systems

              The Mouse Genome Database, (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. MGD data content includes comprehensive characterization of genes and their functions, standardized descriptions of mouse phenotypes, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information including comparative data on mammalian genes. Data within MGD are obtained from diverse sources including manual curation of the biomedical literature, direct contributions from individual investigator's laboratories and major informatics resource centers such as Ensembl, UniProt and NCBI. MGD collaborates with the bioinformatics community on the development of data and semantic standards such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. MGD provides a data-mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the association of gene trap data with mouse genes and a new batch query capability for customized data access and retrieval.
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                Author and article information

                Journal
                Database (Oxford)
                databa
                databa
                Database: The Journal of Biological Databases and Curation
                Oxford University Press
                1758-0463
                2010
                5 August 2010
                5 August 2010
                : 2010
                Affiliations
                1Department of Molecular Genetics, 2Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel, 3Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa, Israel, 4The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel and 5Xennex Inc, Cambridge, MA, USA
                Author notes
                * Corresponding author: Tel: +972 8 934 3455; Fax: +972 8 934 4487. Email: marilyn.safran@ 123456weizmann.ac.il
                Article
                baq020
                10.1093/database/baq020
                2938269
                20689021
                8eee591c-1138-487e-87e7-f65e6ce45c84
                © The Author(s) 2010. Published by Oxford University Press.

                This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Pages: 16
                Categories
                Database Update

                Bioinformatics & Computational biology
                Bioinformatics & Computational biology

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