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Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
Wang, Zichen; Monteiro, Caroline D; Jagodnik, Kathleen M; Fernandez, Nicolas F; Gundersen, Gregory W; Rouillard, Andrew D; Jenkins, Sherry L; Feldmann, Axel S; Hu, Kevin S; McDermott, Michael G; Duan, Qiaonan; Clark, Neil R; Jones, Matthew R; Kou, Yan; Goff, Troy; Woodland, Holly; Amaral, Fabio M R; Szeto, Gregory L; Fuchs, Oliver; Schüssler-Fiorenza Rose, Sophia M; Sharma, Shvetank; Schwartz, Uwe; Bausela, Xabier Bengoetxea; Szymkiewicz, Maciej; Maroulis, Vasileios; Salykin, Anton; Barra, Carolina M; Kruth, Candice D; Bongio, Nicholas J; Mathur, Vaibhav; Todoric, Radmila D; Rubin, Udi E; Malatras, Apostolos; Fulp, Carl T; Galindo, John A; Motiejunaite, Ruta; Jüschke, Christoph; Dishuck, Philip C; Lahl, Katharina; Jafari, Mohieddin; Aibar, Sara; Zaravinos, Apostolos; Steenhuizen, Linda H; Allison, Lindsey R; Gamallo, Pablo; de Andres Segura, Fernando; Dae Devlin, Tyler; Pérez-García, Vicente; Ma'ayan, Avi.
Afiliação
  • Wang Z; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Monteiro CD; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Jagodnik KM; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Fernandez NF; Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd, Cleveland, Ohio 44135, USA.
  • Gundersen GW; Center for Space Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA.
  • Rouillard AD; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Jenkins SL; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Feldmann AS; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Hu KS; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • McDermott MG; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Duan Q; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Clark NR; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Jones MR; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Kou Y; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Goff T; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Woodland H; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Amaral FMR; Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA.
  • Szeto GL; Daylesford, the Fairway, Weybridge, Surrey KT13 0RZ, UK.
  • Fuchs O; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK.
  • Schüssler-Fiorenza Rose SM; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
  • Sharma S; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
  • Schwartz U; Department of Materials Science &Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
  • Bausela XB; The Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, Massachusetts 02139, USA.
  • Szymkiewicz M; Paediatric Allergology and Pulmonology, Dr von Hauner University Children's Hospital, Ludwig-Maximilians-University of Munich, Member of the German Centre for Lung Research (DZL), Lindwurmstrasse 4, Munich 80337, Germany.
  • Maroulis V; Spinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.
  • Salykin A; Department of Neurosurgery, Stanford School of Medicine, Stanford, California 94304, USA.
  • Barra CM; Department of Research, Institute of Liver &Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India.
  • Kruth CD; Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany.
  • Bongio NJ; Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain.
  • Mathur V; Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01-447, Poland.
  • Rubin UE; Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic.
  • Malatras A; IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain.
  • Galindo JA; Department of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA.
  • Motiejunaite R; IBM India Pvt Ltd., Bengaluru 560045, India.
  • Dishuck PC; Department of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA.
  • Lahl K; Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France.
  • Aibar S; Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia.
  • Zaravinos A; Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.
  • Steenhuizen LH; Department of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany.
  • Gamallo P; Technical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark.
  • de Andres Segura F; Protein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, No. 358, 12th Farwardin Ave, Jomhhoori St, Tehran 13164, Iran.
  • Dae Devlin T; School of Biological Sciences, Institute for Researches in Fundamental Sciences, Niavaran Square, P.O.Box, Tehran 19395-5746, Iran.
  • Pérez-García V; University of Salamanca, Salamanca, Madrid 37008, Spain.
  • Ma'ayan A; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, level 7, Stockholm SE141 86, Sweden.
Nat Commun ; 7: 12846, 2016 Sep 26.
Article em En | MEDLINE | ID: mdl-27667448
ABSTRACT
Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO). Through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbation signatures. All these signatures are unique and are manually validated for quality. Global analysis of these signatures confirms known associations and identifies novel associations between genes, diseases and drugs. The manually curated signatures are used as a training set to develop classifiers for extracting similar signatures from the entire GEO repository. We develop a web portal to serve these signatures for query, download and visualization.
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2016 Tipo de documento: Article
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2016 Tipo de documento: Article