Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
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.
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.
Zichen
http://orcid.org/0000-0002-1415-1286
Z
Wang
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.
Caroline D
CD
Monteiro
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.|Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd, Cleveland, Ohio 44135, USA.|Center for Space Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA.
Kathleen M
KM
Jagodnik
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.
Nicolas F
NF
Fernandez
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.
Gregory W
GW
Gundersen
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.
Andrew D
AD
Rouillard
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.
Sherry L
SL
Jenkins
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.
Axel S
AS
Feldmann
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.
Kevin S
KS
Hu
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.
Michael G
MG
McDermott
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.
Qiaonan
Q
Duan
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.
Neil R
NR
Clark
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.
Matthew R
MR
Jones
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.
Yan
Y
Kou
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.
Troy
T
Goff
Daylesford, the Fairway, Weybridge, Surrey KT13 0RZ, UK.
Holly
H
Woodland
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK.
Fabio M R
FMR
Amaral
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|Department of Materials Science &Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|The Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, Massachusetts 02139, USA.
Gregory L
http://orcid.org/0000-0001-7604-1333
GL
Szeto
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.
Oliver
http://orcid.org/0000-0002-7127-5226
O
Fuchs
Spinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.|Department of Neurosurgery, Stanford School of Medicine, Stanford, California 94304, USA.
Sophia M
SM
Schüssler-Fiorenza Rose
Department of Research, Institute of Liver &Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India.
Shvetank
S
Sharma
Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany.
Uwe
U
Schwartz
Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain.
Xabier Bengoetxea
XB
Bausela
Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01-447, Poland.
Maciej
http://orcid.org/0000-0003-1469-9396
M
Szymkiewicz
Vasileios
V
Maroulis
Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic.
Anton
A
Salykin
IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain.
Carolina M
CM
Barra
Candice D
CD
Kruth
Department of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA.
Nicholas J
NJ
Bongio
IBM India Pvt Ltd., Bengaluru 560045, India.
Vaibhav
V
Mathur
Radmila D
RD
Todoric
Department of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA.
Udi E
UE
Rubin
Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France.
Apostolos
A
Malatras
Carl T
CT
Fulp
Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia.
John A
JA
Galindo
Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.
Ruta
R
Motiejunaite
Department of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany.
Christoph
C
Jüschke
Philip C
http://orcid.org/0000-0003-2223-9787
PC
Dishuck
Technical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark.
Katharina
K
Lahl
Protein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, No. 358, 12th Farwardin Ave, Jomhhoori St, Tehran 13164, Iran.|School of Biological Sciences, Institute for Researches in Fundamental Sciences, Niavaran Square, P.O.Box, Tehran 19395-5746, Iran.
Mohieddin
M
Jafari
University of Salamanca, Salamanca, Madrid 37008, Spain.
Sara
http://orcid.org/0000-0001-6104-7134
S
Aibar
Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, level 7, Stockholm SE141 86, Sweden.|Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenes Str. Engomi, P.O.Box 22006, Nicosia 1516, Cyprus.
Apostolos
http://orcid.org/0000-0003-4625-5562
A
Zaravinos
Anna Blamansingel 216, Amsterdam 102 SW, Netherlands.
Linda H
LH
Steenhuizen
Lindsey R
http://orcid.org/0000-0001-9980-4436
LR
Allison
Pablo
P
Gamallo
CICAB, Clinical Research Centre, Extremadura University Hospital, Elvas Av., s/n. 06006 Badajoz 06006, Spain.
Fernando
F
de Andres Segura
Tyler
T
Dae Devlin
Consejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología, Department of Immunology and Oncology, c/Darwin, 3 Madrid 28049, Spain.
Vicente
V
Pérez-García
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.
Avi
A
Ma'ayan
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