miRGator: An integrated system for functional annotation of microRNAs

Seungyoon Nam, Bumjin Kim, Seokmin Shin, Sanghyuk Lee

Research output: Contribution to journalArticlepeer-review

139 Scopus citations


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.

Original languageEnglish
Pages (from-to)D159-D164
JournalNucleic Acids Research
Issue numberSUPPL. 1
StatePublished - Jan 2008

Bibliographical note

Funding Information:
This work was supported by a grant (No. 20070401034010) from BioGreen 21 Program of the Korean Rural Development Administration and by the Korean Ministry of Science and Technology through the bioinformatics research program. B.K. is grateful for the BK21 research fellowship from the Ministry of Education and Human Resources Development. Funding to pay the Open Access publication charges for this article was provided by the Korean Rural Development Administration.


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