Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-09-26

AUTHORS

Zichen Wang, Caroline D. Monteiro, Kathleen M. Jagodnik, Nicolas F. Fernandez, Gregory W. Gundersen, Andrew D. Rouillard, Sherry L. Jenkins, Axel S. Feldmann, Kevin S. Hu, Michael G. McDermott, Qiaonan Duan, Neil R. Clark, Matthew R. Jones, Yan Kou, Troy Goff, Holly Woodland, Fabio M R. Amaral, Gregory L. Szeto, Oliver Fuchs, Sophia M. Schüssler-Fiorenza Rose, Shvetank Sharma, Uwe Schwartz, Xabier Bengoetxea Bausela, Maciej Szymkiewicz, Vasileios Maroulis, Anton Salykin, Carolina M. Barra, Candice D. Kruth, Nicholas J. Bongio, Vaibhav Mathur, Radmila D Todoric, Udi E. Rubin, Apostolos Malatras, Carl T. Fulp, John A. Galindo, Ruta Motiejunaite, Christoph Jüschke, Philip C. Dishuck, Katharina Lahl, Mohieddin Jafari, Sara Aibar, Apostolos Zaravinos, Linda H. Steenhuizen, Lindsey R. Allison, Pablo Gamallo, Fernando de Andres Segura, Tyler Dae Devlin, Vicente Pérez-García, Avi Ma'ayan

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. More... »

PAGES

12846

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  • Journal

    TITLE

    Nature Communications

    ISSUE

    1

    VOLUME

    7

    Author Affiliations

  • 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
  • Center for Space Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
  • Daylesford, the Fairway, Weybridge, Surrey KT13 0RZ, UK
  • School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK
  • The Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, Massachusetts 02139, USA
  • 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
  • Department of Neurosurgery, Stanford School of Medicine, Stanford, California 94304, USA
  • Department of Research, Institute of Liver & Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India
  • Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
  • Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain
  • Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01–447, Poland
  • Plomariou 1 St, 15126 Athens, Greece
  • Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
  • IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain
  • Hailey Ln, Apt C-11, Strasburg, Virginia 22657, USA
  • Department of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA
  • IBM India Pvt Ltd., Bengaluru 560045, India
  • Dr Aleksandra Sijacica 20, Backa Topola 24300, Serbia
  • Department of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA
  • Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France
  • Higashi 4-chome Shibuya-ku, Tokyo 150-0011, Japan
  • Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia
  • Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
  • Department of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany
  • ST NW #2, Washington DC 20007, USA
  • Technical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark
  • School of Biological Sciences, Institute for Researches in Fundamental Sciences, Niavaran Square, P.O.Box, Tehran 19395-5746, Iran
  • University of Salamanca, Salamanca, Madrid 37008, Spain
  • Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenes Str. Engomi, P.O.Box 22006, Nicosia 1516, Cyprus
  • Anna Blamansingel 216, Amsterdam 102 SW, Netherlands
  • Brompton #6024, Houston, Texas 77025, USA
  • Aligustre 30 1-C, Madrid 28039, Spain
  • CICAB, Clinical Research Centre, Extremadura University Hospital, Elvas Av., s/n. 06006 Badajoz 06006, Spain
  • Brown Street, Box 8278, Providence, Rhode Island 02912, USA
  • Consejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología, Department of Immunology and Oncology, c/Darwin, 3 Madrid 28049, Spain
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ncomms12846

    DOI

    http://dx.doi.org/10.1038/ncomms12846

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1041243869

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27667448


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