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

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 w...

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Autores principales:	Yi-An Chen, Lokesh P Tripathi, Kenji Mizuguchi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1cc49e4be4854ec0bdb12ea91ff9393f
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spelling	oai:doaj.org-article:1cc49e4be4854ec0bdb12ea91ff9393f2021-11-18T06:57:41ZTargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.1932-620310.1371/journal.pone.0017844https://doaj.org/article/1cc49e4be4854ec0bdb12ea91ff9393f2011-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21408081/?tool=EBIhttps://doaj.org/toc/1932-6203Prioritising 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/.Yi-An ChenLokesh P TripathiKenji MizuguchiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 3, p e17844 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yi-An Chen Lokesh P Tripathi Kenji Mizuguchi TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
description	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/.
format	article
author	Yi-An Chen Lokesh P Tripathi Kenji Mizuguchi
author_facet	Yi-An Chen Lokesh P Tripathi Kenji Mizuguchi
author_sort	Yi-An Chen
title	TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
title_short	TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
title_full	TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
title_fullStr	TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
title_full_unstemmed	TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
title_sort	targetmine, an integrated data warehouse for candidate gene prioritisation and target discovery.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/1cc49e4be4854ec0bdb12ea91ff9393f
work_keys_str_mv	AT yianchen targetmineanintegrateddatawarehouseforcandidategeneprioritisationandtargetdiscovery AT lokeshptripathi targetmineanintegrateddatawarehouseforcandidategeneprioritisationandtargetdiscovery AT kenjimizuguchi targetmineanintegrateddatawarehouseforcandidategeneprioritisationandtargetdiscovery
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TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.

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