Beegle: from literature mining to disease-gene discovery
Identifieur interne : 000029 ( France/Analysis ); précédent : 000028; suivant : 000030Beegle: from literature mining to disease-gene discovery
Auteurs : Sarah Elshal [Belgique] ; Léon-Charles Tranchevent [Belgique, France] ; Alejandro Sifrim [Belgique, Royaume-Uni] ; Amin Ardeshirdavani [Belgique] ; Jesse Davis [Belgique] ; Yves Moreau [Belgique]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2015.
Abstract
Disease-gene identification is a challenging process that has multiple applications within functional genomics and personalized medicine. Typically, this process involves both finding genes known to be associated with the disease (through literature search) and carrying out preliminary experiments or screens (e.g. linkage or association studies, copy number analyses, expression profiling) to determine a set of promising candidates for experimental validation. This requires extensive time and monetary resources. We describe
Url:
DOI: 10.1093/nar/gkv905
PubMed: 26384564
PubMed Central: 4737179
Affiliations:
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last="Elshal">Sarah Elshal</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">iMinds Future Health Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>iMinds Future Health Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation></author><author><name sortKey="Tranchevent, Leon Charles" sort="Tranchevent, Leon Charles" uniqKey="Tranchevent L" first="Léon-Charles" last="Tranchevent">Léon-Charles Tranchevent</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">iMinds Future Health Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>iMinds Future Health Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF3">Inserm UMR-S1052, CNRS UMR5286, Cancer Research Centre of Lyon, Lyon, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Inserm UMR-S1052, CNRS UMR5286, Cancer Research Centre of Lyon, Lyon</wicri:regionArea><placeName><settlement type="city">Lyon</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Université de Lyon 1, Villeurbanne, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université de Lyon 1, Villeurbanne</wicri:regionArea><placeName><settlement type="city">Villeurbanne</settlement><settlement type="city" wicri:auto="agglo">Lyon</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF5">Centre Léon Bérard, Lyon, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Centre Léon Bérard, Lyon</wicri:regionArea><placeName><settlement type="city">Lyon</settlement></placeName></affiliation></author><author><name sortKey="Sifrim, Alejandro" sort="Sifrim, Alejandro" uniqKey="Sifrim A" first="Alejandro" last="Sifrim">Alejandro Sifrim</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">iMinds Future Health Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>iMinds Future Health Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF6">Wellcome Trust Genome Campus, Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Genome Campus, Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SA</wicri:noRegion></affiliation></author><author><name sortKey="Ardeshirdavani, Amin" sort="Ardeshirdavani, Amin" uniqKey="Ardeshirdavani A" first="Amin" last="Ardeshirdavani">Amin Ardeshirdavani</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">iMinds Future Health Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>iMinds Future Health Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation></author><author><name sortKey="Davis, Jesse" sort="Davis, Jesse" uniqKey="Davis J" first="Jesse" last="Davis">Jesse Davis</name><affiliation wicri:level="1"><nlm:aff id="AFF7">Department of Computer Science (DTAI), KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Computer Science (DTAI), KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation></author><author><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">iMinds Future Health Department, KU Leuven, Leuven 3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>iMinds Future Health Department, KU Leuven, Leuven 3001</wicri:regionArea><wicri:noRegion>Leuven 3001</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Disease-gene identification is a challenging process that has multiple applications within functional genomics and personalized medicine. Typically, this process involves both finding genes known to be associated with the disease (through literature search) and carrying out preliminary experiments or screens (e.g. linkage or association studies, copy number analyses, expression profiling) to determine a set of promising candidates for experimental validation. This requires extensive time and monetary resources. We describe <italic>Beegle</italic>, an online search and discovery engine that attempts to simplify this process by automating the typical approaches. It starts by mining the literature to quickly extract a set of genes known to be linked with a given query, then it integrates the learning methodology of <italic>Endeavour</italic> (a gene prioritization tool) to train a genomic model and rank a set of candidate genes to generate novel hypotheses. In a realistic evaluation setup, <italic>Beegle</italic> has an average recall of 84% in the top 100 returned genes as a search engine, which improves the discovery engine by 12.6% in the top 5% prioritized genes. <italic>Beegle</italic> is publicly available at <ext-link ext-link-type="uri" xlink:href="http://beegle.esat.kuleuven.be/">http://beegle.esat.kuleuven.be/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Perez Iratxeta, C" uniqKey="Perez Iratxeta C">C. Perez-Iratxeta</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P. Bork</name></author><author><name sortKey="Andrade, M A" uniqKey="Andrade M">M.A. Andrade</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moody, S E" uniqKey="Moody S">S.E. Moody</name></author><author><name sortKey="Boehm, J S" uniqKey="Boehm J">J.S. Boehm</name></author><author><name sortKey="Barbie, D A" uniqKey="Barbie D">D.A. 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Vermeesch</name></author><author><name sortKey="Aerts, J" uniqKey="Aerts J">J. Aerts</name></author><author><name sortKey="De Moor, B" uniqKey="De Moor B">B. De Moor</name></author><author><name sortKey="Moreau, Y" uniqKey="Moreau Y">Y. Moreau</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li><li>France</li><li>Royaume-Uni</li></country><settlement><li>Lyon</li><li>Villeurbanne</li></settlement></list><tree><country name="Belgique"><noRegion><name sortKey="Elshal, Sarah" sort="Elshal, Sarah" uniqKey="Elshal S" first="Sarah" last="Elshal">Sarah Elshal</name></noRegion><name sortKey="Ardeshirdavani, Amin" sort="Ardeshirdavani, Amin" uniqKey="Ardeshirdavani A" first="Amin" last="Ardeshirdavani">Amin Ardeshirdavani</name><name sortKey="Ardeshirdavani, Amin" sort="Ardeshirdavani, Amin" uniqKey="Ardeshirdavani A" first="Amin" last="Ardeshirdavani">Amin Ardeshirdavani</name><name sortKey="Davis, Jesse" sort="Davis, Jesse" uniqKey="Davis J" first="Jesse" last="Davis">Jesse Davis</name><name sortKey="Elshal, Sarah" sort="Elshal, Sarah" uniqKey="Elshal S" first="Sarah" last="Elshal">Sarah Elshal</name><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><name sortKey="Sifrim, Alejandro" sort="Sifrim, Alejandro" uniqKey="Sifrim A" first="Alejandro" last="Sifrim">Alejandro Sifrim</name><name sortKey="Sifrim, Alejandro" sort="Sifrim, Alejandro" uniqKey="Sifrim A" first="Alejandro" last="Sifrim">Alejandro Sifrim</name><name sortKey="Tranchevent, Leon Charles" sort="Tranchevent, Leon Charles" uniqKey="Tranchevent L" first="Léon-Charles" last="Tranchevent">Léon-Charles Tranchevent</name><name sortKey="Tranchevent, Leon Charles" sort="Tranchevent, Leon Charles" uniqKey="Tranchevent L" first="Léon-Charles" last="Tranchevent">Léon-Charles Tranchevent</name></country><country name="France"><noRegion><name sortKey="Tranchevent, Leon Charles" sort="Tranchevent, Leon Charles" uniqKey="Tranchevent L" first="Léon-Charles" last="Tranchevent">Léon-Charles Tranchevent</name></noRegion><name sortKey="Tranchevent, Leon Charles" sort="Tranchevent, Leon Charles" uniqKey="Tranchevent L" first="Léon-Charles" last="Tranchevent">Léon-Charles Tranchevent</name><name sortKey="Tranchevent, Leon Charles" sort="Tranchevent, Leon Charles" uniqKey="Tranchevent L" first="Léon-Charles" last="Tranchevent">Léon-Charles Tranchevent</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Sifrim, Alejandro" sort="Sifrim, Alejandro" uniqKey="Sifrim A" first="Alejandro" last="Sifrim">Alejandro Sifrim</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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