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 been...

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Authors: Muniategui, A. (Ander)|||/items/bf5e030f-7e6e-4d2d-bc38-05db5bdc66bf, Nogales-Cadenas, R. (Rubén)|||/items/10ce31b5-bd01-433e-86aa-fb789ce2c54f, Vazquez, M. (Miguel)|||/items/4e12f8a4-7837-4a29-9be2-c9b4e2f8972b, Aranguren-López, X. (Xabier)|||/items/217519c3-f392-48cb-b4c9-87d4e2fd0570, Aguirre-Ena, X. (Xabier)|||/items/2a000d9c-cb5c-4734-a32c-4fef79998c86, Luttun, A. (Aernout)|||/items/8803b530-2d11-42e0-824f-415e53e3dcc6, Prosper-Cardoso, F. (Felipe)|||/items/3d1b0b82-06c3-4e63-8280-e903dc4dc0c1, Pascual-Montano, A. (Alberto)|||/items/645b3a8d-3a55-4e9b-b0bc-d849b5a90f41, Rubio, M.Á. (Miguel Ángel)|||/items/eb2aa544-6f12-497a-9999-10b671c0b3d1
Format: article
Publication Date:2012
Country:España
Institution:Universidad de Navarra
Repository:Dadun. Depósito Académico Digital de la Universidad de Navarra
Language:English
OAI Identifier:oai:dadun.unav.edu:10171/121893
Online Access:https://hdl.handle.net/10171/121893
Access Level:Open access
Keyword:miRNAs
RNA molecules
miRNA-mRNA
LASSO regression
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network_name_str España
repository_id_str
spelling Quantification of miRNA-mRNA InteractionsMuniategui, A. (Ander)|||/items/bf5e030f-7e6e-4d2d-bc38-05db5bdc66bfNogales-Cadenas, R. (Rubén)|||/items/10ce31b5-bd01-433e-86aa-fb789ce2c54fVazquez, M. (Miguel)|||/items/4e12f8a4-7837-4a29-9be2-c9b4e2f8972bAranguren-López, X. (Xabier)|||/items/217519c3-f392-48cb-b4c9-87d4e2fd0570Aguirre-Ena, X. (Xabier)|||/items/2a000d9c-cb5c-4734-a32c-4fef79998c86Luttun, A. (Aernout)|||/items/8803b530-2d11-42e0-824f-415e53e3dcc6Prosper-Cardoso, F. (Felipe)|||/items/3d1b0b82-06c3-4e63-8280-e903dc4dc0c1Pascual-Montano, A. (Alberto)|||/items/645b3a8d-3a55-4e9b-b0bc-d849b5a90f41Rubio, M.Á. (Miguel Ángel)|||/items/eb2aa544-6f12-497a-9999-10b671c0b3d1miRNAsRNA moleculesmiRNA-mRNALASSO regressionmiRNAs 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.PLOSDadun. Depósito Académico Digital Universidad de Navarra20122012-01-0120122012-01-01journal articlehttp://purl.org/coar/resource_type/c_6501info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10171/121893reponame:Dadun. Depósito Académico Digital de la Universidad de Navarrainstname:Universidad de NavarraInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:dadun.unav.edu:10171/1218932026-06-21T12:47:57Z
dc.title.none.fl_str_mv Quantification of miRNA-mRNA Interactions
title Quantification of miRNA-mRNA Interactions
spellingShingle Quantification of miRNA-mRNA Interactions
Muniategui, A. (Ander)|||/items/bf5e030f-7e6e-4d2d-bc38-05db5bdc66bf
miRNAs
RNA molecules
miRNA-mRNA
LASSO regression
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
dc.creator.none.fl_str_mv Muniategui, A. (Ander)|||/items/bf5e030f-7e6e-4d2d-bc38-05db5bdc66bf
Nogales-Cadenas, R. (Rubén)|||/items/10ce31b5-bd01-433e-86aa-fb789ce2c54f
Vazquez, M. (Miguel)|||/items/4e12f8a4-7837-4a29-9be2-c9b4e2f8972b
Aranguren-López, X. (Xabier)|||/items/217519c3-f392-48cb-b4c9-87d4e2fd0570
Aguirre-Ena, X. (Xabier)|||/items/2a000d9c-cb5c-4734-a32c-4fef79998c86
Luttun, A. (Aernout)|||/items/8803b530-2d11-42e0-824f-415e53e3dcc6
Prosper-Cardoso, F. (Felipe)|||/items/3d1b0b82-06c3-4e63-8280-e903dc4dc0c1
Pascual-Montano, A. (Alberto)|||/items/645b3a8d-3a55-4e9b-b0bc-d849b5a90f41
Rubio, M.Á. (Miguel Ángel)|||/items/eb2aa544-6f12-497a-9999-10b671c0b3d1
author Muniategui, A. (Ander)|||/items/bf5e030f-7e6e-4d2d-bc38-05db5bdc66bf
author_facet Muniategui, A. (Ander)|||/items/bf5e030f-7e6e-4d2d-bc38-05db5bdc66bf
Nogales-Cadenas, R. (Rubén)|||/items/10ce31b5-bd01-433e-86aa-fb789ce2c54f
Vazquez, M. (Miguel)|||/items/4e12f8a4-7837-4a29-9be2-c9b4e2f8972b
Aranguren-López, X. (Xabier)|||/items/217519c3-f392-48cb-b4c9-87d4e2fd0570
Aguirre-Ena, X. (Xabier)|||/items/2a000d9c-cb5c-4734-a32c-4fef79998c86
Luttun, A. (Aernout)|||/items/8803b530-2d11-42e0-824f-415e53e3dcc6
Prosper-Cardoso, F. (Felipe)|||/items/3d1b0b82-06c3-4e63-8280-e903dc4dc0c1
Pascual-Montano, A. (Alberto)|||/items/645b3a8d-3a55-4e9b-b0bc-d849b5a90f41
Rubio, M.Á. (Miguel Ángel)|||/items/eb2aa544-6f12-497a-9999-10b671c0b3d1
author_role author
author2 Nogales-Cadenas, R. (Rubén)|||/items/10ce31b5-bd01-433e-86aa-fb789ce2c54f
Vazquez, M. (Miguel)|||/items/4e12f8a4-7837-4a29-9be2-c9b4e2f8972b
Aranguren-López, X. (Xabier)|||/items/217519c3-f392-48cb-b4c9-87d4e2fd0570
Aguirre-Ena, X. (Xabier)|||/items/2a000d9c-cb5c-4734-a32c-4fef79998c86
Luttun, A. (Aernout)|||/items/8803b530-2d11-42e0-824f-415e53e3dcc6
Prosper-Cardoso, F. (Felipe)|||/items/3d1b0b82-06c3-4e63-8280-e903dc4dc0c1
Pascual-Montano, A. (Alberto)|||/items/645b3a8d-3a55-4e9b-b0bc-d849b5a90f41
Rubio, M.Á. (Miguel Ángel)|||/items/eb2aa544-6f12-497a-9999-10b671c0b3d1
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Dadun. Depósito Académico Digital Universidad de Navarra
dc.subject.none.fl_str_mv miRNAs
RNA molecules
miRNA-mRNA
LASSO regression
topic miRNAs
RNA molecules
miRNA-mRNA
LASSO regression
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.
publishDate 2012
dc.date.none.fl_str_mv 2012
2012-01-01
2012
2012-01-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/10171/121893
url https://hdl.handle.net/10171/121893
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv PLOS
publisher.none.fl_str_mv PLOS
dc.source.none.fl_str_mv reponame:Dadun. Depósito Académico Digital de la Universidad de Navarra
instname:Universidad de Navarra
instname_str Universidad de Navarra
reponame_str Dadun. Depósito Académico Digital de la Universidad de Navarra
collection Dadun. Depósito Académico Digital de la Universidad de Navarra
repository.name.fl_str_mv
repository.mail.fl_str_mv
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