TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery
TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery
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DOI：
10.1371/journal.pone.0017844
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发表时间：
2011-03-08
期刊：
影响因子：
3.7
通讯作者：
Mizuguchi, Kenji
中科院分区：
文献类型：
--
作者：
Chen, Yi-An;Tripathi, Lokesh P.;Mizuguchi, Kenji
在药物发现和生物医学研究中，为进一步的实验表征确定候选基因的优先顺序是一项重要的挑战。综合多种数据类型的结果的集成方法最适合于最优目标选择。我们开发了TargetMine，这是一个有效的目标优先级数据仓库。TargetMine利用InterMine框架，以一种新颖的方式集成了新的数据模型，如蛋白质- dna相互作用。它支持难以用现有工具执行的复杂搜索，还提供了自定义注释和内部实验数据的集成。我们使用TargetMine提出了一个目标优先级的客观协议，并建立了一个基准程序来评估其性能。结果表明，该方案可以识别已知的疾病相关基因，具有较高的精度和覆盖率。TargetMine的演示版本可在http://targetmine.nibio.go.jp/上获得。
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/.