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This article is part of the supplement: European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

Open Access Proceedings

Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application

Maria G Roubelakis12, Pantelis Zotos134, Georgios Papachristoudis35, Ioannis Michalopoulos3, Kalliopi I Pappa126, Nicholas P Anagnou12 and Sophia Kossida3*

Author Affiliations

1 Cell & Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece

2 Laboratory of Biology, University of Athens School of Medicine, Athens, Greece

3 Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece

4 Ecole Polytechnique Fédérale de Lausanne, Switzerland

5 MIT Computer Science and Artificial Intelligence Laboratory, The Stata Center, Building 32, 32 Vassar Street, Cambridge, MA 02139, USA

6 First Department of Obstetrics and Gynecology, University of Athens School of Medicine, Athens, Greece

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BMC Bioinformatics 2009, 10(Suppl 6):S20  doi:10.1186/1471-2105-10-S6-S20

Published: 16 June 2009

Abstract

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.