title: Functional microRNA targets in protein coding sequences.
abstract: BACKGROUND
  Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.
  
  
  RESULTS
  Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3(')-untranslated regions (3(')-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3(')-UTR target sites. Further analysis indicates that genes with shorter 3(')-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3(')-UTR.
authors.affiliation: Institute of Molecular Oncology, Biomedical Sciences Research Center, Vari, Greece. reczko@fleming.gr
authors.forename: Martin
authors.initials: M
authors.lastname: Reczko
authors.forename: Manolis
authors.initials: M
authors.lastname: Maragkakis
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Alexiou
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
authors.forename: Artemis G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D020413:3' Untranslated Regions; D000465:Algorithms; D000818:Animals; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016366:Open Reading Frames; D038621:Regulatory Sequences, Ribonucleic Acid
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D038621:Regulatory Sequences, Ribonucleic Acid