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

  • Jesse D. Ziebarth
  • Anindya Bhattacharya
  • Yan Cui
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

SNPs Mutations miRNA targets GWAS eQTLs 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Jesse D. Ziebarth
    • 1
    • 2
  • Anindya Bhattacharya
    • 3
  • Yan Cui
    • 1
    • 2
  1. 1.Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisUSA
  2. 2.Center for Integrative and Translational GenomicsUniversity of Tennessee Health Science CenterMemphisUSA
  3. 3.Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoUSA

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