Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.
TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks
1 Genomic Knowledge Base Research Team, Bioinformatics Group, Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan and 2 Bioinformatics Group, Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
Received on January 15, 2004; accepted on March 1, 2004
Motivation: Most ordinary traits are well described by multiple measurable parameters. Thus, in the course of elucidating the genes responsible for a given trait, it is necessary to conduct and integrate the genetic mapping of each parameter. However, the integration of multiple mapping results from different publications is prevented by the fact that they are conventionally published and accumulated in printed forms or graphics which are difficult for computers to reuse for further analyses.
Results: We have defined an XML-based schema as a container of genetic mapping results, and created a database named TraitMap containing curator-checked data records based on published papers of mapping results in Homosapiens, Mus musculus, and Arabidopsis thaliana. TraitMap is the first database of mapping charts in genetics, and is integrated in a web-based retrieval framework: termed Genome 
Phenome Superhighway (GPS) system, where it is possible to combine and visualize multiple mapping records in a two-dimensional display. Since most traits are regulated by multiple genes, the system associates every combination of genetic loci to biomolecular networks, and thus helps us to estimate molecular-level candidate networks responsible for a given trait. It is demonstrated that a combined analysis of two diabetes-related traits (susceptibility to insulin resistance and non-HDL cholesterol level) suggests that molecular-level relationships such as the interaction among leptin receptor (Lepr), peroxisome proliferators-activated receptor-gamma (Pparg) and insulin receptor substrate 1 (Irs1), are candidate causal networks affecting the traits in a multigenic manner.
Availability: TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/
Supplementary information: See http://omicspace.riken.jp/info/traitmap.html
Contact: toyop{at}gsc.riken.jp
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, these authors should be regarded as joint First Authors.
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