mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts
Program in Molecular Medicine
Animals; Binding Sites; Caenorhabditis elegans; Carrier Proteins; MicroRNAs; RNA, Messenger; Ribonucleoproteins
Biochemistry | Computational Biology | Molecular Biology | Molecular Genetics
Target prediction for animal microRNAs (miRNAs) has been hindered by the small number of verified targets available to evaluate the accuracy of predicted miRNA-target interactions. Recently, a dataset of 3,404 miRNA-associated mRNA transcripts was identified by immunoprecipitation of the RNA-induced silencing complex components AIN-1 and AIN-2. Our analysis of this AIN-IP dataset revealed enrichment for defining characteristics of functional miRNA-target interactions, including structural accessibility of target sequences, total free energy of miRNA-target hybridization and topology of base-pairing to the 5' seed region of the miRNA. We used these enriched characteristics as the basis for a quantitative miRNA target prediction method, miRNA targets by weighting immunoprecipitation-enriched parameters (mirWIP), which optimizes sensitivity to verified miRNA-target interactions and specificity to the AIN-IP dataset. MirWIP can be used to capture all known conserved miRNA-mRNA target relationships in Caenorhabditis elegans at a lower false-positive rate than can the current standard methods.
DOI of Published Version
Nat Methods. 2008 Sep;5(9):813-9. doi: 10.1038/nmeth.1247. Link to article on publisher's site
Hammell, Molly; Long, Dang; Zhang, Liang; Lee, Andrew; Carmack, C. Steven; Han, Min; Ding, Ye; and Ambros, Victor R., "mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts" (2008). Program in Molecular Medicine Publications and Presentations. 36.