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PLoS One. 2011 Mar 8;6(3):e17844. doi: 10.1371/journal.pone.0017844.

TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.

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1
National Institute of Biomedical Innovation, Saito-Asagi, Ibaraki, Osaka, Japan.

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/.

PMID:
21408081
PMCID:
PMC3050930
DOI:
10.1371/journal.pone.0017844
[Indexed for MEDLINE]
Free PMC Article
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