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

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


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Databases, Genetic*
  • Disease / genetics
  • Genetic Association Studies / methods*
  • Humans
  • Protein Structure, Tertiary
  • Software*
  • Transcription Factors / metabolism


  • Transcription Factors