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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents



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ID: 312514.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse
Authors:Nord, Alex S.; Chang, Patricia J.; Conklin, Bruce R.; Cox, Antony V.; Harper, Courtney A.; Hicks, Geoffrey G.; Huang, Conrad C.; Johns, Susan J.; Kawamoto, Michiko; Liu, Songyan; Meng, Elaine C.; Morris, John H.; Rossant, Janet; Ruiz, Patricia; Skarnes, William C.; Soriano, Philippe; Stanford, William L.; Stryke, Doug; von Melchner, Harald; Wurst, Wolfgang; Yamamura, Ken-Ichi; Young, Stephen G.; Babbitt, Patricia C.; Ferrin, Thomas E.
Language:English
Date of Publication (YYYY-MM-DD):2006
Title of Journal:Nucleic Acids Research
Journal Abbrev.:Nucleic Acids Res
Volume:24
Issue / Number:Database issue
Start Page:D642
End Page:D648
Copyright:© 2007 Oxford University Press
Review Status:not specified
Audience:Experts Only
Abstract / Description:Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising ~45 000 well-characterized ES cell lines which currently represent ~40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website (www.genetrap.org) allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function.
Comment of the Author/Creator:e-mail: tef@cgl.ucsf.edu
External Publication Status:published
Document Type:Article
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA;
Gladstone Institute of Cardiovascular Disease, University of California San Francisco Department of Medicine and Pharmacology 1650 Owens Street, San Francisco, CA 94158, USA;
Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK;
Manitoba Institute of Cell Biology, University of Manitoba 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9;
The Hospital for Sick Children Toronto, Ontario, Canada M5G 1X8;
Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA;
University of Toronto 4 Taddle Creek Road, Toronto, Ontario, Canada M5S 3G9;
Department of Molecular Hematology, University of Frankfurt Medical School 60590 Frankfurt am Main, Germany;
GSF Research Center for Environment and Health, Institute for Developmental Genetics Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany;
Institute of Molecular Embryology and Genetics, Kumamoto University 2-2-1 Honjo, Kumamoto 860-0811, Japan;
University of California Los Angeles, 650 Charles E. Young Dr So., Los Angeles, CA 90095, USA
Identifiers:ISSN:0305-1048
DOI:10.1093/nar/gkj097
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