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Computational and Experimental Identification of Tissue-Specific MicroRNA Targets

  • Raheleh Amirkhah
  • Hojjat Naderi Meshkin
  • Ali Farazmand
  • John E. J. Rasko
  • Ulf Schmitz
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1580)

Abstract

In this chapter we discuss computational methods for the prediction of microRNA (miRNA) targets. More specifically, we consider machine learning-based approaches and explain why these methods have been relatively unsuccessful in reducing the number of false positive predictions. Further we suggest approaches designed to improve their performance by considering tissue-specific target regulation. We argue that the miRNA targetome differs depending on the tissue type and introduce a novel algorithm that predicts miRNA targets specifically for colorectal cancer. We discuss features of miRNAs and target sites that affect target recognition, and how next-generation sequencing data can support the identification of novel miRNAs, differentially expressed miRNAs and their tissue-specific mRNA targets. In addition, we introduce some experimental approaches for the validation of miRNA targets as well as web-based resources sharing predicted and validated miRNA target interactions.

Key words

MicroRNA Computational target prediction Machine learning Next-generation sequencing Cross-linking and immunoprecipitation 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Raheleh Amirkhah
    • 1
  • Hojjat Naderi Meshkin
    • 2
  • Ali Farazmand
    • 3
  • John E. J. Rasko
    • 4
  • Ulf Schmitz
    • 4
  1. 1.Reza Institute of Cancer Bioinformatics and Personalized MedicineMashhadIran
  2. 2.Stem Cells and Regenerative Medicine Research GroupAcademic Center for Education, Culture Research (ACECR)MashhadIran
  3. 3.Department of Cell and Molecular Biology, School of Biology, College of ScienceUniversity of TehranTehranIran
  4. 4.Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown; Sydney Medical SchoolUniversity of SydneyCamperdownAustralia

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