Advertisement

microRNA Target Prediction

  • William RitchieEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1513)

Abstract

microRNAs are short RNAs that reduce gene expression by binding to their targets. Computational predictions indicate that all human genes may be regulated by microRNAs, with each microRNA possibly targeting thousands of genes. Commonly used software will produce a prohibitive number of predicted targets for each microRNA. Here I describe procedures that refine these predictions by integrating available software and expression data from experiments available online. These procedures are tailored to experiments where predicting true targets is more important than detecting all putative targets.

Key words

microRNA Target genes microRNA expression 

References

  1. 1.
    Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854Google Scholar
  2. 2.
    Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30:363–364. doi: 10.1038/ng865 CrossRefPubMedGoogle Scholar
  3. 3.
    Ritchie W, Flamant S, Rasko JE (2009) Predicting microRNA targets and functions: traps for the unwary. Nat Methods 6:397–398. doi: 10.1038/nmeth0609-397, nmeth0609-397 [pii]CrossRefPubMedGoogle Scholar
  4. 4.
    Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105. doi: 10.1101/gr.082701.108, gr.082701.108 [pii]CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    John B, Enright AJ, Aravin A et al (2004) Human MicroRNA targets. PLoS Biol 2:e363CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Fan X, Kurgan L (2014) Comprehensive overview and assessment of computational prediction of microRNA targets in animals. Brief Bioinform 16:780–794. doi: 10.1093/bib/bbu044 CrossRefPubMedGoogle Scholar
  7. 7.
    Ritchie W, Flamant S, Rasko JE (2010) mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics 26:223–227. doi: 10.1093/bioinformatics/btp649, btp649 [pii]CrossRefPubMedGoogle Scholar
  8. 8.
    Krek A, Grün D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495–500CrossRefPubMedGoogle Scholar
  9. 9.
    Lim LP, Lau NC, Garrett-Engele P et al (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–773CrossRefPubMedGoogle Scholar
  10. 10.
    Ritchie W, Rajasekhar M, Flamant S, Rasko JE (2009) Conserved expression patterns predict microRNA targets. PLoS Comput Biol 5:e1000513. doi: 10.1371/journal.pcbi.1000513 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Alexiou P, Maragkakis M, Papadopoulos GL et al (2009) Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25:3049–3055. doi: 10.1093/bioinformatics/btp565 CrossRefPubMedGoogle Scholar
  12. 12.
    Xiao F, Zuo Z, Cai G et al (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37:D105–D110. doi: 10.1093/nar/gkn851 CrossRefPubMedGoogle Scholar
  13. 13.
    Yang JH, Li JH, Shao P et al (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39:D202–D209. doi: 10.1093/nar/gkq1056 CrossRefPubMedGoogle Scholar
  14. 14.
    Vergoulis T, Vlachos IS, Alexiou P et al (2012) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 40:D222–D229. doi: 10.1093/nar/gkr1161 CrossRefPubMedGoogle Scholar
  15. 15.
    Lewis BP, Shih IH, Jones-Rhoades MW et al (2003) Prediction of mammalian microRNA targets. Cell 115:787–798, doi:S0092867403010183 [pii]CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.CNRS, UMR 5203MontpellierFrance

Personalised recommendations