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Reexamining microRNA site accessibility in Drosophila: a population genomics study.
Max Delbrück Centrum für Molekulare Medizin, Berlin-Buch, Germany.
2009 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 4, no 5Article in journal (Refereed) Published
Abstract [en]

Kertesz et al. (Nature Genetics 2008) described PITA, a miRNA target prediction algorithm based on hybridization energy and site accessibility. In this note, we used a population genomics approach to reexamine their data and found that the PITA algorithm had lower specificity than methods based on evolutionary conservation at comparable levels of sensitivity.We also showed that deeply conserved miRNAs tend to have stronger hybridization energies to their targets than do other miRNAs. Although PITA had higher specificity in predicting targets than a naïve seed-match method, this signal was primarily due to the use of a single cutoff score for all miRNAs and to the observed correlation between conservation and hybridization energy. Overall, our results clarify the accuracy of different miRNA target prediction algorithms in Drosophila and the role of site accessibility in miRNA target prediction.

Place, publisher, year, edition, pages
Public Library of Science , 2009. Vol. 4, no 5
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:kth:diva-178202DOI: 10.1371/journal.pone.0005681ISI: 000266331700009PubMedID: 19478854Scopus ID: 2-s2.0-66249100252OAI: oai:DiVA.org:kth-178202DiVA: diva2:877727
Note

QC 20160118

Available from: 2015-12-07 Created: 2015-12-07 Last updated: 2017-12-01Bibliographically approved

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