Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application
Author(s)
Roubelakis, Maria G.; Zotos, Pantelis; Papachristoudis, Georgios; Michalopoulos, Ioannis; Pappa, Kalliopi I.; Anagnou, Nicholas P.; Kossida, Sophia; ... Show more Show less
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Background: microRNAs (miRNAs) are single-stranded RNA molecules of about 20–23
nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by
interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit
translation. Predicting or verifying mRNA targets of specific miRNAs is a difficult process of great
importance.
Results: GOmir is a novel stand-alone application consisting of two separate tools: JTarget and
TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the
predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as
well as the experimentally supported targets from TarBase and also providing a full gene
description and functional analysis for each target gene. On the other hand, TAGGO application is
designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology
(GO), in order to extract the main attributes of sets of proteins. GOmir represents a new tool
incorporating two separate Java applications integrated into one stand-alone Java application.
Conclusion: GOmir (by using up to five different databases) introduces miRNA predicted targets
accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology
clustering. Additionally, a reverse search initiated by a potential target can also be conducted.
GOmir can freely be downloaded BRFAA.
Date issued
2009-06Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Electrical Engineering and Computer ScienceJournal
BMC Bioinformatics
Publisher
BioMed Central Ltd.
Citation
Roubelakis, Maria, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi Pappa, Nicholas Anagnou, and Sophia Kossida. 2009. Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application. BMC Bioinformatics 10, no. Suppl 6: S20.
Version: Final published version
ISSN
1471-2105