title: Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Cell & Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece. mroubelaki@bioacademy.gr
authors.forename: Maria G
authors.initials: MG
authors.lastname: Roubelakis
authors.forename: Pantelis
authors.initials: P
authors.lastname: Zotos
authors.forename: Georgios
authors.initials: G
authors.lastname: Papachristoudis
authors.forename: Ioannis
authors.initials: I
authors.lastname: Michalopoulos
authors.forename: Kalliopi I
authors.initials: KI
authors.lastname: Pappa
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Anagnou
authors.forename: Sophia
authors.initials: S
authors.lastname: Kossida
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs