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Computational and Experimental Identification of Tissue-Specific MicroRNA Targets

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MicroRNA Detection and Target Identification

Part of the book series: Methods in Molecular Biology ((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.

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Authors and Affiliations

  1. Reza Institute of Cancer Bioinformatics and Personalized Medicine, Mashhad, Iran

    Raheleh Amirkhah

  2. Stem Cells and Regenerative Medicine Research Group, Academic Center for Education, Culture Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran

    Hojjat Naderi Meshkin

  3. Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran

    Ali Farazmand

  4. Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown; Sydney Medical School, University of Sydney, Camperdown, NSW, 2050, Australia

    John E. J. Rasko & Ulf Schmitz

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  1. Raheleh Amirkhah
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  2. Hojjat Naderi Meshkin
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  3. Ali Farazmand
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  4. John E. J. Rasko
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  5. Ulf Schmitz
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Correspondence to Ulf Schmitz .

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  1. School of Biological Sciences, University of East Anglia, Norwich, United Kingdom

    Tamas Dalmay

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Amirkhah, R., Meshkin, H.N., Farazmand, A., Rasko, J.E.J., Schmitz, U. (2017). Computational and Experimental Identification of Tissue-Specific MicroRNA Targets. In: Dalmay, T. (eds) MicroRNA Detection and Target Identification. Methods in Molecular Biology, vol 1580. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6866-4_11

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  • DOI: https://doi.org/10.1007/978-1-4939-6866-4_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6864-0

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