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dc.contributor.authorAgarwal, Vikram
dc.contributor.authorBell, George W
dc.contributor.authorNam, Jin-Wu
dc.contributor.authorBartel, David
dc.date.accessioned2015-09-29T19:31:39Z
dc.date.available2015-09-29T19:31:39Z
dc.date.issued2015-08
dc.date.submitted2014-10
dc.identifier.issn2050-084X
dc.identifier.urihttp://hdl.handle.net/1721.1/99103
dc.description.abstractMicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.en_US
dc.description.sponsorshipNational Science Foundation (U.S.). Graduate Research Fellowshipen_US
dc.description.sponsorshipNational Institutes of Health (U.S.) (Grant GM067031)en_US
dc.language.isoen_US
dc.publishereLife Sciences Publications, Ltd.en_US
dc.relation.isversionofhttp://dx.doi.org/10.7554/elife.05005en_US
dc.rightsCreative Commons Attributionen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceAgarwalen_US
dc.titlePredicting effective microRNA target sites in mammalian mRNAsen_US
dc.typeArticleen_US
dc.identifier.citationAgarwal, Vikram, George W Bell, Jin-Wu Nam, and David P Bartel. “Predicting Effective microRNA Target Sites in Mammalian mRNAs.” eLife 4 (August 12, 2015).en_US
dc.contributor.departmentMassachusetts Institute of Technology. Computational and Systems Biology Programen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biologyen_US
dc.contributor.departmentWhitehead Institute for Biomedical Researchen_US
dc.contributor.approverAgarwal, Vikramen_US
dc.contributor.mitauthorAgarwal, Vikramen_US
dc.contributor.mitauthorNam, Jin-Wuen_US
dc.contributor.mitauthorBartel, Daviden_US
dc.relation.journaleLifeen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dspace.orderedauthorsAgarwal, Vikram; Bell, George W; Nam, Jin-Wu; Bartel, David Pen_US
dc.identifier.orcidhttps://orcid.org/0000-0001-8148-952X
dc.identifier.orcidhttps://orcid.org/0000-0002-3872-2856
mit.licensePUBLISHER_CCen_US


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