title: TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
abstract: Prioritising candidate genes for further experimental characterisation is a non-trivial challenge in drug discovery and biomedical research in general. An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation. TargetMine utilises the InterMine framework, with new data models such as protein-DNA interactions integrated in a novel way. It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. We proposed an objective protocol for target prioritisation using TargetMine and set up a benchmarking procedure to evaluate its performance. The results show that the protocol can identify known disease-associated genes with high precision and coverage. A demonstration version of TargetMine is available at http://targetmine.nibio.go.jp/.
authors.affiliation: National Institute of Biomedical Innovation, Saito-Asagi, Ibaraki, Osaka, Japan.
authors.forename: Yi-An
authors.initials: YA
authors.lastname: Chen
authors.forename: Lokesh P
authors.initials: LP
authors.lastname: Tripathi
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics; D056726:Genetic Association Studies / Q000379:methods*; D006801:Humans; D017434:Protein Structure, Tertiary; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors