Quantification of miRNA-mRNA interactions.

miRNAs are small RNA molecules (' 22nt) that interact with their corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have...

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Autores principales:	Ander Muniategui, Rubén Nogales-Cadenas, Miguél Vázquez, Xabier L Aranguren, Xabier Agirre, Aernout Luttun, Felipe Prosper, Alberto Pascual-Montano, Angel Rubio
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2caafa8f3d9849b2a130987011696966
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id	oai:doaj.org-article:2caafa8f3d9849b2a130987011696966
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spelling	oai:doaj.org-article:2caafa8f3d9849b2a1309870116969662021-11-18T07:28:23ZQuantification of miRNA-mRNA interactions.1932-620310.1371/journal.pone.0030766https://doaj.org/article/2caafa8f3d9849b2a1309870116969662012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22348024/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203miRNAs are small RNA molecules (' 22nt) that interact with their corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have been deployed, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Recently, it has been proposed to combine expression measurement from both miRNA and mRNA and sequence based predictions to achieve more accurate relationships. In our work, we use LASSO regression with non-positive constraints to integrate both sources of information. LASSO enforces the sparseness of the solution and the non-positive constraints restrict the search of miRNA targets to those with down-regulation effects on the mRNA expression. We named this method TaLasso (miRNA-Target LASSO).We used TaLasso on two public datasets that have paired expression levels of human miRNAs and mRNAs. The top ranked interactions recovered by TaLasso are especially enriched (more than using any other algorithm) in experimentally validated targets. The functions of the genes with mRNA transcripts in the top-ranked interactions are meaningful. This is not the case using other algorithms.TaLasso is available as Matlab or R code. There is also a web-based tool for human miRNAs at http://talasso.cnb.csic.es/.Ander MuniateguiRubén Nogales-CadenasMiguél VázquezXabier L ArangurenXabier AgirreAernout LuttunFelipe ProsperAlberto Pascual-MontanoAngel RubioPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e30766 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ander Muniategui Rubén Nogales-Cadenas Miguél Vázquez Xabier L Aranguren Xabier Agirre Aernout Luttun Felipe Prosper Alberto Pascual-Montano Angel Rubio Quantification of miRNA-mRNA interactions.
description	miRNAs are small RNA molecules (' 22nt) that interact with their corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have been deployed, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Recently, it has been proposed to combine expression measurement from both miRNA and mRNA and sequence based predictions to achieve more accurate relationships. In our work, we use LASSO regression with non-positive constraints to integrate both sources of information. LASSO enforces the sparseness of the solution and the non-positive constraints restrict the search of miRNA targets to those with down-regulation effects on the mRNA expression. We named this method TaLasso (miRNA-Target LASSO).We used TaLasso on two public datasets that have paired expression levels of human miRNAs and mRNAs. The top ranked interactions recovered by TaLasso are especially enriched (more than using any other algorithm) in experimentally validated targets. The functions of the genes with mRNA transcripts in the top-ranked interactions are meaningful. This is not the case using other algorithms.TaLasso is available as Matlab or R code. There is also a web-based tool for human miRNAs at http://talasso.cnb.csic.es/.
format	article
author	Ander Muniategui Rubén Nogales-Cadenas Miguél Vázquez Xabier L Aranguren Xabier Agirre Aernout Luttun Felipe Prosper Alberto Pascual-Montano Angel Rubio
author_facet	Ander Muniategui Rubén Nogales-Cadenas Miguél Vázquez Xabier L Aranguren Xabier Agirre Aernout Luttun Felipe Prosper Alberto Pascual-Montano Angel Rubio
author_sort	Ander Muniategui
title	Quantification of miRNA-mRNA interactions.
title_short	Quantification of miRNA-mRNA interactions.
title_full	Quantification of miRNA-mRNA interactions.
title_fullStr	Quantification of miRNA-mRNA interactions.
title_full_unstemmed	Quantification of miRNA-mRNA interactions.
title_sort	quantification of mirna-mrna interactions.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2caafa8f3d9849b2a130987011696966
work_keys_str_mv	AT andermuniategui quantificationofmirnamrnainteractions AT rubennogalescadenas quantificationofmirnamrnainteractions AT miguelvazquez quantificationofmirnamrnainteractions AT xabierlaranguren quantificationofmirnamrnainteractions AT xabieragirre quantificationofmirnamrnainteractions AT aernoutluttun quantificationofmirnamrnainteractions AT felipeprosper quantificationofmirnamrnainteractions AT albertopascualmontano quantificationofmirnamrnainteractions AT angelrubio quantificationofmirnamrnainteractions
_version_	1718423397709381632

Quantification of miRNA-mRNA interactions.

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