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miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets
BACKGROUND: 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 we...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411648/ https://www.ncbi.nlm.nih.gov/pubmed/22870325 http://dx.doi.org/10.1371/journal.pone.0042390 |
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author | Lu, Tzu-Pin Lee, Chien-Yueh Tsai, Mong-Hsun Chiu, Yu-Chiao Hsiao, Chuhsing Kate Lai, Liang-Chuan Chuang, Eric Y. |
author_facet | Lu, Tzu-Pin Lee, Chien-Yueh Tsai, Mong-Hsun Chiu, Yu-Chiao Hsiao, Chuhsing Kate Lai, Liang-Chuan Chuang, Eric Y. |
author_sort | Lu, Tzu-Pin |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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 | Online Article Text |
id | pubmed-3411648 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-34116482012-08-06 miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets Lu, Tzu-Pin Lee, Chien-Yueh Tsai, Mong-Hsun Chiu, Yu-Chiao Hsiao, Chuhsing Kate Lai, Liang-Chuan Chuang, Eric Y. PLoS One Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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/. Public Library of Science 2012-08-01 /pmc/articles/PMC3411648/ /pubmed/22870325 http://dx.doi.org/10.1371/journal.pone.0042390 Text en © 2012 Lu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Lu, Tzu-Pin Lee, Chien-Yueh Tsai, Mong-Hsun Chiu, Yu-Chiao Hsiao, Chuhsing Kate Lai, Liang-Chuan Chuang, Eric Y. miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets |
title | 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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411648/ https://www.ncbi.nlm.nih.gov/pubmed/22870325 http://dx.doi.org/10.1371/journal.pone.0042390 |
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