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miRGator: an integrated system for functional annotation of microRNAs.

Nam S, Kim B, Shin S, Lee S - Nucleic Acids Res. (2007)

Bottom Line: MicroRNAs (miRNAs) constitute an important class of regulators that are involved in various cellular and disease processes.For the expression analysis, miRGator integrates public expression data of miRNA with those of mRNA and protein.Our web implementation supports diverse query types including miRNA name, gene symbol, gene ontology, pathway and disease terms.

View Article: PubMed Central - PubMed

Affiliation: Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea.

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.

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Schematic overview of miRGator system.
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Figure 1: Schematic overview of miRGator system.

Mentions: Figure 1 shows the overview of database integration, analysis flow and web implementation of miRGator. Functional analysis begins with target prediction. We used the miRanda, PicTar and TargetScanS programs whose genome-wide predictions can be downloaded from the miRBase website and the UCSC genome browser tracks. The lists of target mRNAs are tested for statistical over-representation in any functional nodes using hypergeometric distribution of Fisher's exact test. Implemented functional categories include the GO, KEGG/GenMAPP/BioCarta pathways (18,19) and disease ontology of Ingenuity Pathway Analysis.Figure 1.


miRGator: an integrated system for functional annotation of microRNAs.

Nam S, Kim B, Shin S, Lee S - Nucleic Acids Res. (2007)

Schematic overview of miRGator system.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238850&req=5

Figure 1: Schematic overview of miRGator system.
Mentions: Figure 1 shows the overview of database integration, analysis flow and web implementation of miRGator. Functional analysis begins with target prediction. We used the miRanda, PicTar and TargetScanS programs whose genome-wide predictions can be downloaded from the miRBase website and the UCSC genome browser tracks. The lists of target mRNAs are tested for statistical over-representation in any functional nodes using hypergeometric distribution of Fisher's exact test. Implemented functional categories include the GO, KEGG/GenMAPP/BioCarta pathways (18,19) and disease ontology of Ingenuity Pathway Analysis.Figure 1.

Bottom Line: MicroRNAs (miRNAs) constitute an important class of regulators that are involved in various cellular and disease processes.For the expression analysis, miRGator integrates public expression data of miRNA with those of mRNA and protein.Our web implementation supports diverse query types including miRNA name, gene symbol, gene ontology, pathway and disease terms.

View Article: PubMed Central - PubMed

Affiliation: Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea.

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.

Show MeSH