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

Hammell, M., Long, D., Zhang, L., Lee, A., Carmack, C. S., Han, M., Ding, Y., Ambros, V. (September 2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nature Methods, 5 (9). pp. 813-9. ISSN 1548-7091 (Print)1548-7091

URL: http://www.ncbi.nlm.nih.gov/pubmed/19160516
DOI: 10.1038/nmeth.1247

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.

Item Type: Paper
Uncontrolled Keywords: Animals Binding Sites Caenorhabditis elegans/*genetics Carrier Proteins/metabolism MicroRNAs/*genetics/metabolism RNA, Messenger/*genetics Ribonucleoproteins/*genetics
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > nuclear ribonucleoprotein
CSHL Authors:
Communities: CSHL labs > Hammell M. lab
Depositing User: Matt Covey
Date: September 2008
Date Deposited: 06 Nov 2014 19:20
Last Modified: 06 Nov 2014 19:20
PMCID: PMC3092588
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30885

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