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mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts
Program in Molecular Medicine Publications and Presentations
  • Molly Hammell, University of Massachusetts Medical School
  • Dang Long, New York State Department of Health
  • Liang Zhang, Howard Hughes Medical Institute
  • Andrew Lee, University of Massachusetts Medical School Worcester
  • C. Steven Carmack, New York State Department of Health
  • Min Han, Howard Hughes Medical Institute
  • Ye Ding, New York State Department of Health
  • Victor R. Ambros, University of Massachusetts Medical School
UMMS Affiliation
Program in Molecular Medicine
Date
9-1-2008
Document Type
Article
Medical Subject Headings
Animals; Binding Sites; Caenorhabditis elegans; Carrier Proteins; MicroRNAs; RNA, Messenger; Ribonucleoproteins
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.

Comments

Citation: Nat Methods. 2008 Sep;5(9):813-9. doi: 10.1038/nmeth.1247. Link to article on publisher's site

Related Resources
Link to Article in PubMed
PubMed ID
19160516
Citation Information
Molly Hammell, Dang Long, Liang Zhang, Andrew Lee, et al.. "mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts" Vol. 5 Iss. 9 (2008) ISSN: 1548-7091 (Linking)
Available at: http://works.bepress.com/victor_ambros/17/