miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data

Messenger RNAs (mRNAs) fulfil specific biological roles in cells and, thus, their expression may be adapted to suit specific circumstances. This is in part achieved through selective gene transcription and post-transcriptional events, the regulation of which must be tightly integrated and controlled...

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Detalhes bibliográficos
Autores: Andrés-León, Eduardo, Rojas Mendoza, Ana M.
Tipo de documento: artigo
Estado:Versión aceptada para publicación
Data de publicação:2019
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/202265
Acesso em linha:http://hdl.handle.net/10261/202265
Access Level:Acceso aberto
Palavra-chave:miRNA
Small RNASeq analysis
RNASeq analysis
miRNA-mRNA target prediction
Integrative analysis
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spelling miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression dataAndrés-León, EduardoRojas Mendoza, Ana M.miRNASmall RNASeq analysisRNASeq analysismiRNA-mRNA target predictionIntegrative analysisMessenger RNAs (mRNAs) fulfil specific biological roles in cells and, thus, their expression may be adapted to suit specific circumstances. This is in part achieved through selective gene transcription and post-transcriptional events, the regulation of which must be tightly integrated and controlled. To comprehensively study the coordinated effects of transcriptional and post-transcriptional regulatory elements, and to obtain coherent results, it is advisable to use different methodologies. Adequately integrating the data derived from these distinct methodologies then becomes critical to elucidating the relationships between the coordinated cellular effects assayed, particularly when applied to normal and disease states. Such integrated studies are likely to be particularly useful to identify markers suitable for early detection of diseases and to devise strategies for therapeutic interventions. Throughout this chapter, we will focus on the methods currently available to analyse mRNA and microRNA (miRNA) expression, paying special attention to the influence of miRNAs on mRNA metabolism. We will introduce miARma-Seq, a comprehensive pipeline that facilitates the simultaneous integration of mRNA and miRNA expression data. For illustrative purposes, we include a case study that incorporates data from RNASeq and small-RNASeq, detailing all the steps necessary to define the differential expression of both mRNA- and miRNA-encoding genes. Finally, we explore the possible regulatory relationships that drive significant and potentially relevant changes in mRNA and miRNA gene expression.ElsevierAcademic PressConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2020202020192020info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/202265reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1016/j.ymeth.2018.09.002Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2022652026-05-22T06:33:51Z
dc.title.none.fl_str_mv miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
title miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
spellingShingle miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
Andrés-León, Eduardo
miRNA
Small RNASeq analysis
RNASeq analysis
miRNA-mRNA target prediction
Integrative analysis
title_short miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
title_full miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
title_fullStr miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
title_full_unstemmed miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
title_sort miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data
dc.creator.none.fl_str_mv Andrés-León, Eduardo
Rojas Mendoza, Ana M.
author Andrés-León, Eduardo
author_facet Andrés-León, Eduardo
Rojas Mendoza, Ana M.
author_role author
author2 Rojas Mendoza, Ana M.
author2_role author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv miRNA
Small RNASeq analysis
RNASeq analysis
miRNA-mRNA target prediction
Integrative analysis
topic miRNA
Small RNASeq analysis
RNASeq analysis
miRNA-mRNA target prediction
Integrative analysis
description Messenger RNAs (mRNAs) fulfil specific biological roles in cells and, thus, their expression may be adapted to suit specific circumstances. This is in part achieved through selective gene transcription and post-transcriptional events, the regulation of which must be tightly integrated and controlled. To comprehensively study the coordinated effects of transcriptional and post-transcriptional regulatory elements, and to obtain coherent results, it is advisable to use different methodologies. Adequately integrating the data derived from these distinct methodologies then becomes critical to elucidating the relationships between the coordinated cellular effects assayed, particularly when applied to normal and disease states. Such integrated studies are likely to be particularly useful to identify markers suitable for early detection of diseases and to devise strategies for therapeutic interventions. Throughout this chapter, we will focus on the methods currently available to analyse mRNA and microRNA (miRNA) expression, paying special attention to the influence of miRNAs on mRNA metabolism. We will introduce miARma-Seq, a comprehensive pipeline that facilitates the simultaneous integration of mRNA and miRNA expression data. For illustrative purposes, we include a case study that incorporates data from RNASeq and small-RNASeq, detailing all the steps necessary to define the differential expression of both mRNA- and miRNA-encoding genes. Finally, we explore the possible regulatory relationships that drive significant and potentially relevant changes in mRNA and miRNA gene expression.
publishDate 2019
dc.date.none.fl_str_mv 2019
2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/202265
url http://hdl.handle.net/10261/202265
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1016/j.ymeth.2018.09.002
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
Academic Press
publisher.none.fl_str_mv Elsevier
Academic Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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