miRGator: an integrated system for functional annotation of microRNAs.

@article{citeulike:1791621, abstract = {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.}, address = {Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742 and Department of Chemistry, Seoul National University, Seoul 151-742, Korea.}, author = {Nam, Seungyoon and Kim, Bumjin and Shin, Seokmin and Lee, Sanghyuk }, citeulike-article-id = {1791621}, comment = {http://genome.ewha.ac.kr/miRGator}, doi = {http://dx.doi.org/10.1093/nar/gkm829}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {coexpression, correlation, database, expression, functional\_annotation, gene\_set\_analysis, microrna, webserver}, month = {October}, posted-at = {2007-11-12 12:51:36}, priority = {0}, title = {miRGator: an integrated system for functional annotation of microRNAs.}, url = {http://dx.doi.org/10.1093/nar/gkm829}, year = {2007} }

TY - JOUR ID - citeulike:1791621 L3 - citeulike-article-id:1791621 N2 - 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. JF - Nucleic Acids Res SN - 1362-4962 AD - Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742 and Department of Chemistry, Seoul National University, Seoul 151-742, Korea. TI - miRGator: an integrated system for functional annotation of microRNAs. KW - coexpression KW - correlation KW - database KW - expression KW - functional_annotation KW - gene_set_analysis KW - microrna KW - webserver N1 - http://genome.ewha.ac.kr/miRGator AU - Nam, Seungyoon AU - Kim, Bumjin AU - Shin, Seokmin AU - Lee, Sanghyuk PY - 2007/10/16/ UR - http://dx.doi.org/10.1093/nar/gkm829 ER -