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

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 and Avi Ma’ayan ()
Additional contact information
Zichen Wang: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Caroline D. Monteiro: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Kathleen M. Jagodnik: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Nicolas F. Fernandez: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Gregory W. Gundersen: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Andrew D. Rouillard: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Sherry L. Jenkins: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Axel S. Feldmann: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Kevin S. Hu: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Michael G. McDermott: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Qiaonan Duan: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Neil R. Clark: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Matthew R. Jones: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Yan Kou: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Troy Goff: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai
Holly Woodland: Daylesford, the Fairway
Fabio M R. Amaral: School of Biosciences, University of Nottingham, Sutton Bonington Campus
Gregory L. Szeto: Massachusetts Institute of Technology
Oliver Fuchs: 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)
Sophia M. Schüssler-Fiorenza Rose: Spinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System
Shvetank Sharma: Institute of Liver & Biliary Sciences
Uwe Schwartz: University of Regensburg
Xabier Bengoetxea Bausela: University of Navarra
Maciej Szymkiewicz: Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences
Anton Salykin: Faculty of Medicine, Masaryk University
Carolina M. Barra: IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader
Nicholas J. Bongio: Shenandoah University
Vaibhav Mathur: IBM India Pvt Ltd.
Udi E. Rubin: Department of Biological Sciences
Apostolos Malatras: Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617
John A. Galindo: Universidad Nacional de Colombia
Ruta Motiejunaite: Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women’s Hospital
Christoph Jüschke: Faculty of Medicine and Health Sciences, University of Oldenburg
Katharina Lahl: Technical University of Denmark, National Veterinary Institute
Mohieddin Jafari: Protein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran
Sara Aibar: University of Salamanca
Apostolos Zaravinos: Karolinska Institute
Linda H. Steenhuizen: Anna Blamansingel 216
Fernando de Andres Segura: CICAB, Clinical Research Centre, Extremadura University Hospital
Vicente Pérez-García: Consejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología
Avi Ma’ayan: BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai

Nature Communications, 2016, vol. 7, issue 1, 1-11

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms12846

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