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Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study

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  • Kevin Chen
  • Jonas Maaskola
  • Mark L Siegal
  • Nikolaus Rajewsky

Abstract

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.

Suggested Citation

  • Kevin Chen & Jonas Maaskola & Mark L Siegal & Nikolaus Rajewsky, 2009. "Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study," PLOS ONE, Public Library of Science, vol. 4(5), pages 1-5, May.
    • Handle: RePEc:plo:pone00:0005681
    DOI: 10.1371/journal.pone.0005681
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    Cited by:

    1. Parawee Lekprasert & Michael Mayhew & Uwe Ohler, 2011. "Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-13, June.
    2. Ray M Marín & Jiří Vaníček, 2012. "Optimal Use of Conservation and Accessibility Filters in MicroRNA Target Prediction," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-11, February.

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