TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.
BACKGROUND
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.


BACKGROUND
TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/
Heida
Naohiko
N
Genomic Knowledge Base Research Team, Bioinformatics Group, Genomic Sciences Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan.
Hasegawa
Yoshikazu
Y
Mochizuki
Yoshiki
Y
Hirosawa
Katsura
K
Konagaya
Akihiko
A
Toyoda
Tetsuro
T
D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D005810:Multigene Family / Q000235:genetics; D011381:Programming Languages; D025941:Protein Interaction Mapping / Q000379:methods*; D040641:Quantitative Trait Loci / Q000235:genetics*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D018511:Systems Integration