title: The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
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.
authors.affiliation: University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.
authors.forename: Alex S
authors.initials: AS
authors.lastname: Nord
authors.forename: Patricia J
authors.initials: PJ
authors.lastname: Chang
authors.forename: Bruce R
authors.initials: BR
authors.lastname: Conklin
authors.forename: Antony V
authors.initials: AV
authors.lastname: Cox
authors.forename: Courtney A
authors.initials: CA
authors.lastname: Harper
authors.forename: Geoffrey G
authors.initials: GG
authors.lastname: Hicks
authors.forename: Conrad C
authors.initials: CC
authors.lastname: Huang
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Johns
authors.forename: Michiko
authors.initials: M
authors.lastname: Kawamoto
authors.forename: Songyan
authors.initials: S
authors.lastname: Liu
authors.forename: Elaine C
authors.initials: EC
authors.lastname: Meng
authors.forename: John H
authors.initials: JH
authors.lastname: Morris
authors.forename: Janet
authors.initials: J
authors.lastname: Rossant
authors.forename: Patricia
authors.initials: P
authors.lastname: Ruiz
authors.forename: William C
authors.initials: WC
authors.lastname: Skarnes
authors.forename: Philippe
authors.initials: P
authors.lastname: Soriano
authors.forename: William L
authors.initials: WL
authors.lastname: Stanford
authors.forename: Doug
authors.initials: D
authors.lastname: Stryke
authors.forename: Harald
authors.initials: H
authors.lastname: von Melchner
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wurst
authors.forename: Ken-ichi
authors.initials: K
authors.lastname: Yamamura
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Young
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Babbitt
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ferrin
mesh_terms: D000818:Animals; D002460:Cell Line; D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D004622:Embryo, Mammalian / Q000166:cytology; D007391:International Cooperation; D020407:Internet; D051379:Mice / Q000196:embryology / Q000235:genetics*; D018345:Mice, Knockout; D016254:Mutagenesis, Insertional / Q000379:methods; D012333:RNA, Messenger / Q000032:analysis; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger