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Predicting Functional MicroRNA-mRNA Interactions

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MicroRNA Detection and Target Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1580))

Abstract

MicroRNAs (miRNAs) are small RNA molecules that play key regulatory roles in general biological processes and disease pathogenesis. These small RNA molecules interact with their target mRNAs to induce mRNA degradation and/or inhibit the translation of mRNAs into proteins. Therefore, identifying miRNA targets is an essential step to fully understand the regulatory effects of miRNAs. Here, we describe a regularized regression approach that integrates the sequence information with the miRNA and mRNA expression profiles for detecting miRNA targets. This method takes into account the full spectrum of gene sequence features of miRNA targets, including the thermodynamic stability, the accessibility energy, and the context features of the target sites,. Given these sequence features for each putative miRNA-mRNA interaction and their expression values, this model is able to quantify the down-regulation effect of each miRNA on its targets while simultaneously estimating the contribution of each sequence feature for predicting functional miRNA-mRNA interactions.

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Acknowledgment

This work is supported in part by NIH grant R01 LM010022 and the seed grant from the University of Texas Health Science Center at Houston.

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Authors and Affiliations

  1. University of Texas M.D. Anderson Cancer Center, 77455 Fannin Street, Houston, TX, USA

    Zixing Wang

  2. Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, USA

    Yin Liu

  3. University of Texas Graduate School of Biomedical Science, 6767 Bertner Avenue, Houston, TX, USA

    Yin Liu

Authors
  1. Zixing Wang
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  2. Yin Liu
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Corresponding author

Correspondence to Yin Liu .

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Editors and Affiliations

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

    Tamas Dalmay

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Wang, Z., Liu, Y. (2017). Predicting Functional MicroRNA-mRNA Interactions. 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_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6866-4_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6864-0

  • Online ISBN: 978-1-4939-6866-4

  • eBook Packages: Springer Protocols

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