ArticleNature communications2016
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
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In one paragraph
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers, 2 of them syntheses that pooled it.
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166citing papers in PubMed, 2 pooled it
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Who cites it
166 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data.Bioinformatics (Oxford, England) · 2019Pooled it
- Integrating single-cell and bulk transcriptomic perturbation resources reveals complementary therapeutic spaces for drug repurposing.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators.bioRxiv : the preprint server for biology · 2026Article
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- Harnessing AI to fuse phenotypic signatures for drug target identification: progress in computational modeling.Briefings in bioinformatics · 2026Review
- Exploring the role of the key gene TNFAIP3 between periodontitis and influenza A through bioinformatic analysis and molecular docking.PloS one · 2026Article
- A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs.Genomics, proteomics & bioinformatics · 2025Article
- An Application of a Large-Scale, Data-Driven Approach to Prioritize Compound-Targeted Conditions in the Nutraceutical Space: Case Study of QuercefitMolecular nutrition & food research · 2025Article
- CORESH: a gene signature-based search engine for public gene expression datasets.Nucleic acids research · 2025Article
- Drug Search and Design Considering Cell Specificity of Chemically Induced Gene Expression Profiles for Disease-Associated Tissues.Molecular informatics · 2025Article
- Therapeutic target prediction for orphan diseases integrating genome-wide and transcriptome-wide association studies.Nature communications · 2025Article
- Playbook workflow builder: Interactive construction of bioinformatics workflows.PLoS computational biology · 2025Article
- Identification biomarkers and therapeutic targets of disulfidptosis-related in rheumatoid arthritis via bioinformatics, molecular dynamics simulation, and experimental validation.Scientific reports · 2025Article
- SSL-VQ: vector-quantized variational autoencoders for semi-supervised prediction of therapeutic targets across diverse diseases.Bioinformatics (Oxford, England) · 2025Article
- A Computational Recognition Analysis of Promising Prognostic Biomarkers in Breast, Colon and Lung Cancer Patients.International journal of molecular sciences · 2025Article
- Comprehensive evaluation of pure and hybrid collaborative filtering in drug repurposing.Scientific reports · 2025Article
- The novel diagnostic markers for systemic lupus erythematosus and periodontal disease.Frontiers in immunology · 2025Article
- Identification ofJournal of inflammation research · 2025Article
- Article
106 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
49 authors.
Zichen WangDepartment 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.ORCID http://orcid.org/0000-0002-1415-1286
Caroline D MonteiroDepartment 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.
Kathleen M JagodnikDepartment 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 FernandezDepartment 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 GundersenDepartment 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 RouillardDepartment 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 JenkinsDepartment 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 FeldmannDepartment 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 HuDepartment 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 McDermottDepartment 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 DuanDepartment 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 ClarkDepartment 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 JonesDepartment 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 KouDepartment 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 GoffDepartment 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.
Holly WoodlandDaylesford, the Fairway, Weybridge, Surrey KT13 0RZ, UK.
Fabio M R AmaralSchool of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK.
Gregory L SzetoDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.ORCID http://orcid.org/0000-0001-7604-1333
Oliver FuchsPaediatric 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.ORCID http://orcid.org/0000-0002-7127-5226
Sophia M Schüssler-Fiorenza RoseSpinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.
Shvetank SharmaDepartment of Research, Institute of Liver &Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India.
Uwe SchwartzDepartment of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany.
Xabier Bengoetxea BauselaDepartment of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain.
Maciej SzymkiewiczWarsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01-447, Poland.ORCID http://orcid.org/0000-0003-1469-9396
Vasileios Maroulis
Anton SalykinDepartment of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic.
Carolina M BarraIMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain.
Candice D Kruth
Nicholas J BongioDepartment of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA.
Vaibhav MathurIBM India Pvt Ltd., Bengaluru 560045, India.
Radmila D Todoric
Udi E RubinDepartment of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA.
Apostolos MalatrasCenter for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France.
Carl T Fulp
John A GalindoDepartment of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia.
Ruta MotiejunaiteCenter for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.
Christoph JüschkeDepartment of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany.
Philip C DishuckORCID http://orcid.org/0000-0003-2223-9787
Katharina LahlTechnical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark.
Mohieddin JafariProtein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, No. 358, 12th Farwardin Ave, Jomhhoori St, Tehran 13164, Iran.
Sara AibarUniversity of Salamanca, Salamanca, Madrid 37008, Spain.ORCID http://orcid.org/0000-0001-6104-7134
Apostolos ZaravinosDivision of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, level 7, Stockholm SE141 86, Sweden.ORCID http://orcid.org/0000-0003-4625-5562
Linda H SteenhuizenAnna Blamansingel 216, Amsterdam 102 SW, Netherlands.
Lindsey R AllisonORCID http://orcid.org/0000-0001-9980-4436
Pablo Gamallo
Fernando de Andres SeguraCICAB, Clinical Research Centre, Extremadura University Hospital, Elvas Av., s/n. 06006 Badajoz 06006, Spain.
Tyler Dae Devlin
Vicente Pérez-GarcíaConsejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología, Department of Immunology and Oncology, c/Darwin, 3 Madrid 28049, Spain.
Avi Ma'ayanDepartment 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.
Funding
Data Coordination and Integration Center for LINCS-BD2KU54HL127624 · NHLBI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SCHURER, STEPHAN C · 2014 to 2019
$23.5MTRAINING PROGRAM IN MOLECULAR AND CELLULAR CARDIOLOGYT32HL007824 · NHLBI · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI GELB, BRUCE D · 1995 to 2022
$8.6MBinding of Epstein Barr Virus EBNA2 Unifies Multiple Sclerosis Genetic MechanismsR01NS099068 · NINDS · CINCINNATI CHILDRENS HOSP MED CTR · PI Leah Claire Kottyan, Matthew Tyson Weirauch · 2017 to 2026
$4.2MUser Interface PortalU54CA189201 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI DUDLEY, JOEL THOMAS, MA'AYAN, AVI · 2014 to 2017
$1.9MExpression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory LayersR01GM098316 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI · 2012 to 2015
$1.3MNCI NIH HHS U54 CA189201NHLBI NIH HHS T32 HL007824NHLBI NIH HHS U54 HL127624NIGMS NIH HHS R01 GM098316NINDS NIH HHS R01 NS099068
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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What Socratic holds
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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.