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.

Figure 1

IGTC identification and annotation pipeline. IGTC members submit gene trap cell line data to dbGSS. The first step of the IGTC pipeline is the download of all publicly available gene trap cell line data from dbGSS. Gene trap sequences are then processed through the dual identification protocol based on genomic localization and transcript alignment using MapTag and AutoIdent, respectively. Returned homologous genomic regions and transcripts are aligned to genomic sequence to generate confirmed overlapping sequence regions, which are used as the primary identification data. Confirmed genomic coordinates are queried against major informatics databases to obtain annotation data for the genomic locus identified, and the returned data are entered into the IGTC database.

Figure 2

IGTC Website cell line annotation page. The image provides an example of the main data page for gene trap cell lines. Users can view primary identification and annotation data, with a link to detailed reports from the IGTC pipeline. An extensive amount of related annotation data is also presented to give researchers more information about the trapped locus. Finally, the page shows details about the cell line and vector and an image showing all gene trap cell line sequences aligned to the trapped gene. From this page, users are directed to the IGTC member site for cell line requests.

Figure 3

Gene trap data access. Several methods for users to find gene trap cell lines of interest are illustrated.