Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.
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- dc.contributor.author Wang, Zichenca
- dc.contributor.author Barra Quaglia, Carolina M., 1982-ca
- dc.date.accessioned 2016-12-20T12:27:56Z
- dc.date.available 2016-12-20T12:27:56Z
- dc.date.issued 2016
- dc.description.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.ca
- dc.description.sponsorship This work is supported by NIH grants: R01GM098316, U54HL127624 and U54CA189201 to A.M.
- dc.format.mimetype application/pdfca
- dc.identifier.citation Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF Gundersen GW, Rouillard AD. et al. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846ca
- dc.identifier.doi http://dx.doi.org/10.1038/ncomms12846
- dc.identifier.issn 2041-1723
- dc.identifier.uri http://hdl.handle.net/10230/27797
- dc.language.iso engca
- dc.publisher Nature Publishing Groupca
- dc.relation.ispartof Nature Communications. 2016 Sep 26;7:12846
- dc.rights © 2016, The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri https://creativecommons.org/licenses/by/4.0/ca
- dc.subject.other Genèticaca
- dc.title Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.ca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca