miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.

<h4>Background</h4>Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues...

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Autores principales:	Tzu-Pin Lu, Chien-Yueh Lee, Mong-Hsun Tsai, Yu-Chiao Chiu, Chuhsing Kate Hsiao, Liang-Chuan Lai, Eric Y Chuang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/df97f068167143eaa39652b15abfa402
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spelling	oai:doaj.org-article:df97f068167143eaa39652b15abfa4022021-11-18T07:10:02ZmiRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.1932-620310.1371/journal.pone.0042390https://doaj.org/article/df97f068167143eaa39652b15abfa4022012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22870325/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses.<h4>Results</h4>First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted.<h4>Conclusions</h4>MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.Tzu-Pin LuChien-Yueh LeeMong-Hsun TsaiYu-Chiao ChiuChuhsing Kate HsiaoLiang-Chuan LaiEric Y ChuangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e42390 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tzu-Pin Lu Chien-Yueh Lee Mong-Hsun Tsai Yu-Chiao Chiu Chuhsing Kate Hsiao Liang-Chuan Lai Eric Y Chuang miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
description	<h4>Background</h4>Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses.<h4>Results</h4>First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted.<h4>Conclusions</h4>MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.
format	article
author	Tzu-Pin Lu Chien-Yueh Lee Mong-Hsun Tsai Yu-Chiao Chiu Chuhsing Kate Hsiao Liang-Chuan Lai Eric Y Chuang
author_facet	Tzu-Pin Lu Chien-Yueh Lee Mong-Hsun Tsai Yu-Chiao Chiu Chuhsing Kate Hsiao Liang-Chuan Lai Eric Y Chuang
author_sort	Tzu-Pin Lu
title	miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
title_short	miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
title_full	miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
title_fullStr	miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
title_full_unstemmed	miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
title_sort	mirsystem: an integrated system for characterizing enriched functions and pathways of microrna targets.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/df97f068167143eaa39652b15abfa402
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miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.

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