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MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis

BACKGROUND: miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight i...

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Autores principales: Licursi, Valerio, Conte, Federica, Fiscon, Giulia, Paci, Paola
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829817/
https://www.ncbi.nlm.nih.gov/pubmed/31684860
http://dx.doi.org/10.1186/s12859-019-3105-x
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author Licursi, Valerio
Conte, Federica
Fiscon, Giulia
Paci, Paola
author_facet Licursi, Valerio
Conte, Federica
Fiscon, Giulia
Paci, Paola
author_sort Licursi, Valerio
collection PubMed
description BACKGROUND: miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS: We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis. The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target interaction. In addition, the holistic approach of the network theory is used to infer possible evidences of miRNA regulation by capturing emergent properties of the miRNA-target regulatory network that would be not evident through a pairwise analysis of the individual components. CONCLUSION: MIENTURNET offers the possibility to consistently perform both statistical and network-based analyses by using only a single tool leading to a more effective prioritization of the miRNA-target interactions. This has the potential to avoid researchers without computational and informatics skills to navigate multiple websites and thus to independently investigate miRNA activity in every cellular process of interest in an easy and at the same time exhaustive way thanks to the intuitive web interface. The web application along with a well-documented and comprehensive user guide are freely available at http://userver.bio.uniroma1.it/apps/mienturnet/ without any login requirement.
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spelling pubmed-68298172019-11-07 MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis Licursi, Valerio Conte, Federica Fiscon, Giulia Paci, Paola BMC Bioinformatics Software BACKGROUND: miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS: We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis. The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target interaction. In addition, the holistic approach of the network theory is used to infer possible evidences of miRNA regulation by capturing emergent properties of the miRNA-target regulatory network that would be not evident through a pairwise analysis of the individual components. CONCLUSION: MIENTURNET offers the possibility to consistently perform both statistical and network-based analyses by using only a single tool leading to a more effective prioritization of the miRNA-target interactions. This has the potential to avoid researchers without computational and informatics skills to navigate multiple websites and thus to independently investigate miRNA activity in every cellular process of interest in an easy and at the same time exhaustive way thanks to the intuitive web interface. The web application along with a well-documented and comprehensive user guide are freely available at http://userver.bio.uniroma1.it/apps/mienturnet/ without any login requirement. BioMed Central 2019-11-04 /pmc/articles/PMC6829817/ /pubmed/31684860 http://dx.doi.org/10.1186/s12859-019-3105-x Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Licursi, Valerio
Conte, Federica
Fiscon, Giulia
Paci, Paola
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
title MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
title_full MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
title_fullStr MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
title_full_unstemmed MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
title_short MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
title_sort mienturnet: an interactive web tool for microrna-target enrichment and network-based analysis
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829817/
https://www.ncbi.nlm.nih.gov/pubmed/31684860
http://dx.doi.org/10.1186/s12859-019-3105-x
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