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A guide through present computational approaches for the identification of mammalian microRNA targets

Nature Methods volume 3, pages 881–886 (2006)Cite this article

Abstract

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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Figure 1: Three categories of microRNA target sites.
Figure 2: Performance spectrum of target prediction programs.

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Acknowledgements

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).

Author information

Authors and Affiliations

  1. Center for Bioinformatics, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Praveen Sethupathy, Molly Megraw & Artemis G Hatzigeorgiou

  2. Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Praveen Sethupathy, Molly Megraw & Artemis G Hatzigeorgiou

  3. Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Artemis G Hatzigeorgiou

Authors
  1. Praveen Sethupathy
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  2. Molly Megraw
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  3. Artemis G Hatzigeorgiou
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Corresponding author

Correspondence to Artemis G Hatzigeorgiou.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Non-conserved TarBase miRNA-target interactions. (XLS 16 kb)

Supplementary Table 2

Benchmark datasets. (XLS 30 kb)

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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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