Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data

We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target down...

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Detalles Bibliográficos
Autores principales: Liu, Weijun, Wang, Xiaowei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341724/
https://www.ncbi.nlm.nih.gov/pubmed/30670076
http://dx.doi.org/10.1186/s13059-019-1629-z
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author Liu, Weijun
Wang, Xiaowei
author_facet Liu, Weijun
Wang, Xiaowei
author_sort Liu, Weijun
collection PubMed
description We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target downregulation. By integrating these common features in a machine learning framework, we develop and validate an improved computational model for genome-wide miRNA target prediction. All prediction data can be accessed at miRDB (http://mirdb.org). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1629-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-63417242019-01-24 Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data Liu, Weijun Wang, Xiaowei Genome Biol Method We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target downregulation. By integrating these common features in a machine learning framework, we develop and validate an improved computational model for genome-wide miRNA target prediction. All prediction data can be accessed at miRDB (http://mirdb.org). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1629-z) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-22 /pmc/articles/PMC6341724/ /pubmed/30670076 http://dx.doi.org/10.1186/s13059-019-1629-z Text en © The Author(s). 2019 Open AccessThis 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 Method
Liu, Weijun
Wang, Xiaowei
Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
title Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
title_full Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
title_fullStr Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
title_full_unstemmed Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
title_short Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
title_sort prediction of functional microrna targets by integrative modeling of microrna binding and target expression data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341724/
https://www.ncbi.nlm.nih.gov/pubmed/30670076
http://dx.doi.org/10.1186/s13059-019-1629-z
work_keys_str_mv AT liuweijun predictionoffunctionalmicrornatargetsbyintegrativemodelingofmicrornabindingandtargetexpressiondata
AT wangxiaowei predictionoffunctionalmicrornatargetsbyintegrativemodelingofmicrornabindingandtargetexpressiondata

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