Journal Article

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

Tripathi, Lokesh P., Chen, Yi-An, Mizuguchi, Kenji

2011

Overview

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/.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Acids / Animals / Annotations / Bioinformatics / Biology / Computational Biology - methods / Consortia / Data models / Data warehouses / Databases, Genetic / Deoxyribonucleic acid / Disease - genetics / DNA / Drug discovery / Fines & penalties / Flexibility / Gene expression / Genes / Genetic Association Studies - methods / Genomes / Genomics / Hepatitis / Humans / Information retrieval / Integrated approach / Metabolites / Mutation / Ontology / Protein Structure, Tertiary / Proteins / Protocol (computers) / Queries / Relevance / Software / Transcription Factors - metabolism / Warehouse stores