The IKMC database and web site will continue to evolve. We will continue to expand and enhance the representation of vector and mutant allele information. Currently, this information is available for targeted mutants from the EUCOMM and KOMP programs, in a format that combines graphical views and sequence feature files. Including targeted allele information from NorCOMM, and adding a graphical representation of mutant alleles in their genomic context are important pending tasks. We are also completing the storage of targeted allele information from other large-scale targeting programs such as the Sanger Institute microRNA Knockout program (MirKO) and epitope-tagged alleles generated by the EUTRACC consortium (www.eutracc.eu
). Our intent is to expand the targeting repository to include all future, publically-available targeted alleles in the mouse generated from large-scale programs.
The characterization of IKMC gene trap alleles by the TIGM, EUCOMM and NorCOMM programs, as well as other gene traps with sequence tags deposited in the dbGSS library, is now nearing completion, in the form of a Gene Trap Data Repository. Gene trap alleles are characterized using a modified Unitrap (16
) algorithm for sequence-tag mapping and clustering. The definition of these gene-trap alleles not only simplifies the presentation of gene-trap data by condensing multiple gene traps into clusters that express the same fusion transcript, but also allows us to provide mutant allele sequence and graphics using the same methods already developed for targeted mutations. When complete, the Gene Trap Data Repository will form another component of the IKMC database, and its allele information will be served by the IKMC portal alongside the information on targeted mutations.
One particularly exciting aspect of our current and future work is to integrate IKMC targeted alleles with additional biological information from other sources through the use of BioMart technology (17
). A BioMart portal prototype is available on the ‘Prototypes’ tab of the IKMC web site (www.knockoutmouse.org/martsearch
). Currently, this portal combines information on IKMC mouse knockout resources with numerous other relevant datasets, including gene information from MGI and Ensembl, gene expression data from EurExpress (www.eurexpress.org
), phenotype data from Europhenome (18
), and mouse distribution information from EMMA. Work is underway to develop BioMarts of GXD gene expression information (19
), biochemical pathway and human disease associations. Data representation, integration and querying capabilities via the BioMart interface will be refined and data from other resources will be added. This feature will further enhance the utility of IKMC data and help to realize the enormous potential of IKMC resources for future biomedical research.