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

Alexander Nord, Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper, Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto, Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang WurstKen ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, Thomas E. Ferrin

Research output: Contribution to journalArticle

112 Citations (Scopus)

Abstract

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 approximately 45 000 well-characterized ES cell lines which currently represent approximately 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.

Original languageEnglish (US)
JournalNucleic acids research.
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006
Externally publishedYes

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Cell Line
Genes
Embryonic Stem Cells
Computational Biology
Mutant Strains Mice
Databases
Informatics
Knockout Mice
Genome
Mutation

ASJC Scopus subject areas

  • Genetics

Cite this

Nord, A., Chang, P. J., Conklin, B. R., Cox, A. V., Harper, C. A., Hicks, G. G., ... Ferrin, T. E. (2006). The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic acids research., 34(Database issue).

The International Gene Trap Consortium Website : a portal to all publicly available gene trap cell lines in mouse. / Nord, Alexander; 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.

In: Nucleic acids research., Vol. 34, No. Database issue, 01.01.2006.

Research output: Contribution to journalArticle

Nord, A, Chang, PJ, Conklin, BR, Cox, AV, Harper, CA, Hicks, GG, Huang, CC, Johns, SJ, Kawamoto, M, Liu, S, Meng, EC, Morris, JH, Rossant, J, Ruiz, P, Skarnes, WC, Soriano, P, Stanford, WL, Stryke, D, von Melchner, H, Wurst, W, Yamamura, KI, Young, SG, Babbitt, PC & Ferrin, TE 2006, 'The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.', Nucleic acids research., vol. 34, no. Database issue.
Nord, Alexander ; 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. / The International Gene Trap Consortium Website : a portal to all publicly available gene trap cell lines in mouse. In: Nucleic acids research. 2006 ; Vol. 34, No. Database issue.
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abstract = "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 approximately 45 000 well-characterized ES cell lines which currently represent approximately 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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AU - Wurst, Wolfgang

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