Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA–target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.
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We are grateful for the insightful suggestions regarding this study from the reviewers and many of our colleagues. We thank A. Economides, M. Reczko and K. Essien for their helpful comments on the manuscript, and J. Hirel for his help with the extraction of precompiled target predictions from the web. P.S. is supported by a pre-doctoral US National Institutes of Health training grant (5T32GM008216). P.S., M.M. and A.G.H. are supported by a US National Science Foundation Career Award Grant (DBI-0238295).
The authors declare no competing financial interests.
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Sethupathy, P., Megraw, M. & Hatzigeorgiou, A. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3, 881–886 (2006). https://doi.org/10.1038/nmeth954
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