title: The DIANA-mirExTra web server: from gene expression data to microRNA function.
abstract: BACKGROUND
  High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer.
  
  
  RESULTS
  Although miRNA expression levels may not be routinely measured in high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression can be computationally predicted and quantified through analysis of overrepresented motifs in the deregulated genes 3' untranslated region (3'UTR) sequences. Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. To this end, we have investigated different approaches and measures, and have practically implemented them on experimental data.
  
  
  CONCLUSIONS
  On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA. Beyond the prediction of miRNAs responsible for the deregulation of transcripts, the web-server provides extensive links to DIANA-mirPath, a functional analysis tool incorporating miRNA targets in biological pathways. Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.
authors.affiliation: Biomedical Sciences Research Center "Alexander Fleming", Institute of Molecular Oncology, Varkiza, Greece.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Alexiou
authors.forename: Manolis
authors.initials: M
authors.lastname: Maragkakis
authors.forename: Giorgio L
authors.initials: GL
authors.lastname: Papadopoulos
authors.forename: Victor A
authors.initials: VA
authors.lastname: Simmosis
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.forename: Artemis G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics / Q000473:pathology; D012984:Software
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs