Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
Identifieur interne : 000A51 ( Main/Exploration ); précédent : 000A50; suivant : 000A52Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
Auteurs : Benjamin Haibe-Kains [États-Unis] ; Catharina Olsen [Belgique] ; Amira Djebbari [Canada] ; Gianluca Bontempi [Belgique] ; Mick Correll [États-Unis] ; Christopher Bouton [États-Unis] ; John Quackenbush [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2011.
Abstract
Genomics provided us with an unprecedented quantity of data on the genes that are activated or repressed in a wide range of phenotypes. We have increasingly come to recognize that defining the networks and pathways underlying these phenotypes requires both the integration of multiple data types and the development of advanced computational methods to infer relationships between the genes and to estimate the predictive power of the networks through which they interact. To address these issues we have developed
Url:
DOI: 10.1093/nar/gkr1050
PubMed: 22096235
PubMed Central: 3245161
Affiliations:
- Belgique, Canada, États-Unis
- Massachusetts, Ontario, Région de Bruxelles-Capitale
- Bruxelles, Toronto
- Université de Toronto, Université libre de Bruxelles
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Le document en format XML
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Newburyport, MA 01950, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Entagen, Newburyport, MA 01950</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Quackenbush, John" sort="Quackenbush, John" uniqKey="Quackenbush J" first="John" last="Quackenbush">John Quackenbush</name><affiliation><nlm:aff id="gkr1050-AFF1">Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute,</nlm:aff><wicri:noCountry code="subfield">Dana-Farber Cancer Institute</wicri:noCountry></affiliation><affiliation wicri:level="2"><nlm:aff id="gkr1050-AFF1">Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr1050-AFF1">Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston</wicri:cityArea></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="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Genomics provided us with an unprecedented quantity of data on the genes that are activated or repressed in a wide range of phenotypes. We have increasingly come to recognize that defining the networks and pathways underlying these phenotypes requires both the integration of multiple data types and the development of advanced computational methods to infer relationships between the genes and to estimate the predictive power of the networks through which they interact. To address these issues we have developed <italic>Predictive Networks</italic> (PN), a flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ‘known’ interactions together with gene expression data to infer robust gene networks. The PN web application is accessible from <ext-link ext-link-type="uri" xlink:href="http://predictivenetworks.org">http://predictivenetworks.org</ext-link>. The PN code base is freely available at <ext-link ext-link-type="uri" xlink:href="https://sourceforge.net/projects/predictivenets/">https://sourceforge.net/projects/predictivenets/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Spellman, Pt" uniqKey="Spellman P">PT Spellman</name></author><author><name sortKey="Sherlock, G" uniqKey="Sherlock G">G Sherlock</name></author><author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name></author><author><name sortKey="Iyer, Vr" uniqKey="Iyer V">VR Iyer</name></author><author><name sortKey="Anders, K" uniqKey="Anders K">K Anders</name></author><author><name sortKey="Eisen, Mb" uniqKey="Eisen M">MB Eisen</name></author><author><name sortKey="Brown, Po" uniqKey="Brown P">PO Brown</name></author><author><name sortKey="Botstein, D" uniqKey="Botstein D">D Botstein</name></author><author><name sortKey="Futcher, B" uniqKey="Futcher B">B 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uniqKey="Symmans W">WF Symmans</name></author><author><name sortKey="Bardelli, A" uniqKey="Bardelli A">A Bardelli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Culhane, Ac" uniqKey="Culhane A">AC Culhane</name></author><author><name sortKey="Schwarzl, T" uniqKey="Schwarzl T">T Schwarzl</name></author><author><name sortKey="Sultana, R" uniqKey="Sultana R">R Sultana</name></author><author><name sortKey="Picard, Kc" uniqKey="Picard K">KC Picard</name></author><author><name sortKey="Picard, Sc" uniqKey="Picard S">SC Picard</name></author><author><name sortKey="Lu, Th" uniqKey="Lu T">TH Lu</name></author><author><name sortKey="Franklin, Kr" uniqKey="Franklin K">KR Franklin</name></author><author><name sortKey="French, Sj" uniqKey="French S">SJ French</name></author><author><name sortKey="Papenhausen, G" uniqKey="Papenhausen G">G Papenhausen</name></author><author><name sortKey="Correll, M" uniqKey="Correll M">M Correll</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loi, Sm" uniqKey="Loi S">SM Loi</name></author><author><name sortKey="Haibe Kains, B" uniqKey="Haibe Kains B">B Haibe-Kains</name></author><author><name sortKey="Desmedt, C" uniqKey="Desmedt C">C Desmedt</name></author><author><name sortKey="Wirapati, P" uniqKey="Wirapati P">P Wirapati</name></author><author><name sortKey="Lallemand, F" uniqKey="Lallemand F">F Lallemand</name></author><author><name sortKey="Tutt, Am" uniqKey="Tutt A">AM Tutt</name></author><author><name sortKey="Gillet, C" uniqKey="Gillet C">C Gillet</name></author><author><name sortKey="Ellis, P" uniqKey="Ellis P">P Ellis</name></author><author><name sortKey="Ryder, K" uniqKey="Ryder K">K Ryder</name></author><author><name sortKey="Reid, Jf" uniqKey="Reid J">JF Reid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ding, C" uniqKey="Ding C">C Ding</name></author><author><name sortKey="Peng, H" uniqKey="Peng H">H Peng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcgill, Wj" uniqKey="Mcgill W">WJ McGill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, Pe" uniqKey="Meyer P">PE Meyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Neapolitan, Re" uniqKey="Neapolitan R">RE Neapolitan</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li><li>Canada</li><li>États-Unis</li></country><region><li>Massachusetts</li><li>Ontario</li><li>Région de Bruxelles-Capitale</li></region><settlement><li>Bruxelles</li><li>Toronto</li></settlement><orgName><li>Université de Toronto</li><li>Université libre de Bruxelles</li></orgName></list><tree><country name="États-Unis"><region name="Massachusetts"><name sortKey="Haibe Kains, Benjamin" sort="Haibe Kains, Benjamin" uniqKey="Haibe Kains B" first="Benjamin" last="Haibe-Kains">Benjamin Haibe-Kains</name></region><name sortKey="Bouton, Christopher" sort="Bouton, Christopher" uniqKey="Bouton C" first="Christopher" last="Bouton">Christopher Bouton</name><name sortKey="Correll, Mick" sort="Correll, Mick" uniqKey="Correll M" first="Mick" last="Correll">Mick Correll</name><name sortKey="Quackenbush, John" sort="Quackenbush, John" uniqKey="Quackenbush J" first="John" last="Quackenbush">John Quackenbush</name><name sortKey="Quackenbush, John" sort="Quackenbush, John" uniqKey="Quackenbush J" first="John" last="Quackenbush">John Quackenbush</name></country><country name="Belgique"><region name="Région de Bruxelles-Capitale"><name sortKey="Olsen, Catharina" sort="Olsen, Catharina" uniqKey="Olsen C" first="Catharina" last="Olsen">Catharina Olsen</name></region><name sortKey="Bontempi, Gianluca" sort="Bontempi, Gianluca" uniqKey="Bontempi G" first="Gianluca" last="Bontempi">Gianluca Bontempi</name></country><country name="Canada"><region name="Ontario"><name sortKey="Djebbari, Amira" sort="Djebbari, Amira" uniqKey="Djebbari A" first="Amira" last="Djebbari">Amira Djebbari</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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