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Nucleic Acids Research 2006 34(Database Issue):D642-D648; doi:10.1093/nar/gkj097
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Nucleic Acids Research, 2006, Vol. 34, Database issue D642-D648
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse

Alex S. Nord1,3, Patricia J. Chang1, Bruce R. Conklin2, Antony V. Cox3, Courtney A. Harper1, Geoffrey G. Hicks4, Conrad C. Huang1, Susan J. Johns1, Michiko Kawamoto1, Songyan Liu4, Elaine C. Meng1, John H. Morris1, Janet Rossant5, Patricia Ruiz6, William C. Skarnes3, Philippe Soriano7, William L. Stanford8, Doug Stryke1, Harald von Melchner9, Wolfgang Wurst10, Ken-ichi Yamamura11, Stephen G. Young12, Patricia C. Babbitt1 and Thomas E. Ferrin1,*

1University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA 2Gladstone Institute of Cardiovascular Disease, University of California San Francisco Department of Medicine and Pharmacology 1650 Owens Street, San Francisco, CA 94158, USA 3Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK 4Manitoba Institute of Cell Biology, University of Manitoba 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9 5The Hospital for Sick Children Toronto, Ontario, Canada M5G 1X8 6Center for Cardiovascular Research, Charité Universitätsmedizin and Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics 14195 Berlin, Germany 7Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA 8University of Toronto 4 Taddle Creek Road, Toronto, Ontario, Canada M5S 3G9 9Department of Molecular Hematology, University of Frankfurt Medical School 60590 Frankfurt am Main, Germany 10GSF Research Center for Environment and Health, Institute for Developmental Genetics Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany 11Institute of Molecular Embryology and Genetics, Kumamoto University 2-2-1 Honjo, Kumamoto 860-0811, Japan 12University of California Los Angeles, 650 Charles E. Young Dr So., Los Angeles, CA 90095, USA

*To whom correspondence should be addressed. Email: tef{at}cgl.ucsf.edu

Received August 16, 2005. Revised October 7, 2005. Accepted October 16, 2005.

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.


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