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Analysis of MicroRNA Expression Using Machine Learning

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miRNomics: MicroRNA Biology and Computational Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1107))

Abstract

The systematic analysis of miRNA expression and its potential mRNA targets constitutes a basal objective in miRNA research in addition to miRNA gene detection and miRNA target prediction. In this chapter we address methodical issues of miRNA expression analysis using self-organizing maps (SOM), a neural network machine learning algorithm with strong visualization and second-level analysis capabilities widely used to categorize large-scale, high-dimensional data. We shortly review selected experimental and theoretical aspects of miRNA expression analysis. Then, the protocol of our SOM method is outlined with special emphasis on miRNA/mRNA coexpression. The method allows extracting differentially expressed RNA transcripts, their functional context, and also characterization of global properties of expression states and profiles. In addition to the separate study of miRNA and mRNA expression landscapes, we propose the combined analysis of both entities using a covariance SOM.

Henry Wirth and Mehmet Volkan Çakir have contributed equally to this chapter.

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Acknowledgements

This publication is supported by LIFE—Center for Civilization Diseases, Universität Leipzig. LIFE is funded by the European ERDF fund and by the Free State of Saxony.

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Authors and Affiliations

  1. Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany

    Henry Wirth, Mehmet Volkan Çakir, Lydia Hopp & Hans Binder

  2. LIFE Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany

    Henry Wirth, Lydia Hopp & Hans Binder

Authors
  1. Henry Wirth
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  2. Mehmet Volkan Çakir
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  3. Lydia Hopp
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  4. Hans Binder
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Editor information

Editors and Affiliations

  1. Dabburiya Village, Israel

    Malik Yousef

  2. Izmir Institute of Technology, Izmir, Turkey

    Jens Allmer

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Wirth, H., Çakir, M.V., Hopp, L., Binder, H. (2014). Analysis of MicroRNA Expression Using Machine Learning. In: Yousef, M., Allmer, J. (eds) miRNomics: MicroRNA Biology and Computational Analysis. Methods in Molecular Biology, vol 1107. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-748-8_16

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  • DOI: https://doi.org/10.1007/978-1-62703-748-8_16

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-747-1

  • Online ISBN: 978-1-62703-748-8

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