TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi, Vladimir Uversky
2011 PLoS ONE  
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
more » ... hes 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 diseaseassociated genes with high precision and coverage. A demonstration version of TargetMine is available at http://targetmine. nibio.go.jp/.
doi:10.1371/journal.pone.0017844 pmid:21408081 pmcid:PMC3050930 fatcat:fvfqc77ymjfmlmviaqhb6wjkha