Article abstract
Nature Methods 5, 813 - 819 (2008)
Published online: 17 August 2008 | doi:10.1038/nmeth.1247
mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts
Molly Hammell1, Dang Long2, Liang Zhang3, Andrew Lee1, C Steven Carmack2, Min Han3, Ye Ding2 & Victor Ambros1
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.
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Suite 306, Worcester, Massachusetts 01605, USA.
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, New York 12208, USA.
- Howard Hughes Medical Institute, Department of Molecular, Cellular and Developmental Biology, Campus Box 347, University of Colorado at Boulder, Boulder, Colorado 80309, USA.
Correspondence to: Victor Ambros1 e-mail: vrambros@gmail.com
Correspondence to: Ye Ding2 e-mail: yding@wadsworth.org
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