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miRGator: an integrated system for functional annotation of microRNAs

MicroRNAs (miRNAs) constitute an important class of regulators that are involved in various cellular and disease processes. However, the functional significance of each miRNA is mostly unknown due to the difficulty in identifying target genes and the lack of genome-wide expression data combining miR...

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Detalles Bibliográficos
Autores principales: Nam, Seungyoon, Kim, Bumjin, Shin, Seokmin, Lee, Sanghyuk
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238850/
https://www.ncbi.nlm.nih.gov/pubmed/17942429
http://dx.doi.org/10.1093/nar/gkm829
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author Nam, Seungyoon
Kim, Bumjin
Shin, Seokmin
Lee, Sanghyuk
author_facet Nam, Seungyoon
Kim, Bumjin
Shin, Seokmin
Lee, Sanghyuk
author_sort Nam, Seungyoon
collection PubMed
description MicroRNAs (miRNAs) constitute an important class of regulators that are involved in various cellular and disease processes. However, the functional significance of each miRNA is mostly unknown due to the difficulty in identifying target genes and the lack of genome-wide expression data combining miRNAs, mRNAs and proteins. We introduce a novel database, miRGator, that integrates the target prediction, functional analysis, gene expression data and genome annotation. MiRNA function is inferred from the list of target genes predicted by miRanda, PicTar and TargetScanS programs. Statistical enrichment test of target genes in each term is performed for gene ontology, pathway and disease annotations. Associated terms may provide valuable insights for the function of each miRNA. For the expression analysis, miRGator integrates public expression data of miRNA with those of mRNA and protein. Expression correlation between miRNA and target mRNA/proteins is evaluated and their expression patterns can be readily compared. Our web implementation supports diverse query types including miRNA name, gene symbol, gene ontology, pathway and disease terms. Interfaces for exploring common targets or regulatory miRNAs and for profiling compendium expression data have been developed as well. Currently, miRGator, available at: http://genome.ewha.ac.kr/miRGator/, supports the human and mouse genomes.
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spelling pubmed-22388502008-02-12 miRGator: an integrated system for functional annotation of microRNAs Nam, Seungyoon Kim, Bumjin Shin, Seokmin Lee, Sanghyuk Nucleic Acids Res Articles MicroRNAs (miRNAs) constitute an important class of regulators that are involved in various cellular and disease processes. However, the functional significance of each miRNA is mostly unknown due to the difficulty in identifying target genes and the lack of genome-wide expression data combining miRNAs, mRNAs and proteins. We introduce a novel database, miRGator, that integrates the target prediction, functional analysis, gene expression data and genome annotation. MiRNA function is inferred from the list of target genes predicted by miRanda, PicTar and TargetScanS programs. Statistical enrichment test of target genes in each term is performed for gene ontology, pathway and disease annotations. Associated terms may provide valuable insights for the function of each miRNA. For the expression analysis, miRGator integrates public expression data of miRNA with those of mRNA and protein. Expression correlation between miRNA and target mRNA/proteins is evaluated and their expression patterns can be readily compared. Our web implementation supports diverse query types including miRNA name, gene symbol, gene ontology, pathway and disease terms. Interfaces for exploring common targets or regulatory miRNAs and for profiling compendium expression data have been developed as well. Currently, miRGator, available at: http://genome.ewha.ac.kr/miRGator/, supports the human and mouse genomes. Oxford University Press 2008-01 2007-10-16 /pmc/articles/PMC2238850/ /pubmed/17942429 http://dx.doi.org/10.1093/nar/gkm829 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Nam, Seungyoon
Kim, Bumjin
Shin, Seokmin
Lee, Sanghyuk
miRGator: an integrated system for functional annotation of microRNAs
title miRGator: an integrated system for functional annotation of microRNAs
title_full miRGator: an integrated system for functional annotation of microRNAs
title_fullStr miRGator: an integrated system for functional annotation of microRNAs
title_full_unstemmed miRGator: an integrated system for functional annotation of microRNAs
title_short miRGator: an integrated system for functional annotation of microRNAs
title_sort mirgator: an integrated system for functional annotation of micrornas
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238850/
https://www.ncbi.nlm.nih.gov/pubmed/17942429
http://dx.doi.org/10.1093/nar/gkm829
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