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Nat Methods. 2008 Sep;5(9):813-9. doi: 10.1038/nmeth.1247.

mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts.

Author information

  • 1Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Suite 306, Worcester, Massachusetts 01605, USA.

Abstract

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.

PMID:
19160516
[PubMed - indexed for MEDLINE]
PMCID:
PMC3092588
Free PMC Article

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