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Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources

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MicroRNA Target Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1970))

Abstract

MicroRNAs are small noncoding RNA molecules with great importance in regulating a large number of diverse biological processes in health and disease. MicroRNAs can bind to both coding and noncoding RNAs and regulate their stability and expression. Genetic variants and somatic mutations may alter microRNA sequences and their target sites and therefore impact microRNA–target recognition. Aberrant microRNA–target interactions have been associated with many diseases. In recent years, computational resources have been developed for retrieving, annotating, and analyzing the impact of mutations on microRNA–target recognition. In this chapter, we provide an overview on the computational analysis of mutations impacting microRNA target recognition, followed by a detailed tutorial on how to use three major Web-based bioinformatics resources: PolymiRTS (http://compbio.uthsc.edu/miRSNP), a database of genetic variants impacting microRNA target recognition; SomamiR (http://compbio.uthsc.edu/SomamiR), a database of somatic mutations affecting the interactions between microRNAs and their targets in mRNAs and noncoding RNAs; and miR2GO (http://compbio.uthsc.edu/miR2GO), a computational tool for knowledge-based functional analysis of genetic variants and somatic mutations in microRNA seed regions.

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Authors and Affiliations

  1. Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA

    Jesse D. Ziebarth & Yan Cui

  2. Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN, USA

    Jesse D. Ziebarth & Yan Cui

  3. Department of Computer Science and Engineering, University of California, San Diego, CA, USA

    Anindya Bhattacharya

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  1. Jesse D. Ziebarth
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  2. Anindya Bhattacharya
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  3. Yan Cui
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  1. Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA

    Alessandro Laganà

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Ziebarth, J.D., Bhattacharya, A., Cui, Y. (2019). Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources. In: Laganà, A. (eds) MicroRNA Target Identification. Methods in Molecular Biology, vol 1970. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9207-2_8

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  • DOI: https://doi.org/10.1007/978-1-4939-9207-2_8

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