spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
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- dc.contributor.author Furió-Tarí, Pedroca
- dc.contributor.author Tarazona, Soniaca
- dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
- dc.contributor.author Enright, Anton J.ca
- dc.contributor.author Conesa, Anaca
- dc.date.accessioned 2017-01-25T07:49:16Z
- dc.date.available 2017-01-25T07:49:16Z
- dc.date.issued 2016ca
- dc.description.abstract Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs.
- dc.description.sponsorship This work was supported by grant FP7 STATegra project [agreement number 36000]; MINECO, co-funded with European Regional Development Funds (ERDF) [BIO2012-40244]; European Molecular Biology Laboratory and the European Union and ERC Seventh Framework Programme (FP7/2007-2013) [ERC-2012-StG-310325].
- dc.format.mimetype application/pdfca
- dc.identifier.citation Furió-Tarí P, Tarazona S, Gabaldón Estevan JA, Enright AJ, Conesa A. spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Research. 2016;44(W1):W176-W180. DOI: 10.1093/nar/gkw443ca
- dc.identifier.doi http://dx.doi.org/10.1093/nar/gkw443
- dc.identifier.issn 0305-1048ca
- dc.identifier.uri http://hdl.handle.net/10230/27981
- dc.language.iso engca
- dc.publisher Oxford University Pressca
- dc.relation.ispartof Nucleic Acids Research. 2016;44(W1):W176-W180
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2012-40244
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/36000
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/310325
- dc.rights © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.subject.keyword RNA
- dc.subject.keyword Messenger
- dc.subject.keyword Surgical sponges
- dc.subject.keyword Micro RNA
- dc.title spongeScan: A web for detecting microRNA binding elements in lncRNA sequencesca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca