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

Jesse D. Ziebarth, Anindya Bhattacharya, Yan Cui

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages101-120
Number of pages20
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume1970
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Computational Biology
MicroRNAs
Mutation
Untranslated RNA
Genetic Databases
Biological Phenomena
Small Untranslated RNA
Seeds
Databases
Messenger RNA
Health

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Ziebarth, J. D., Bhattacharya, A., & Cui, Y. (2019). Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources. In Methods in Molecular Biology (pp. 101-120). (Methods in Molecular Biology; Vol. 1970). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9207-2_8

Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition : Bioinformatics Resources. / Ziebarth, Jesse D.; Bhattacharya, Anindya; Cui, Yan.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 101-120 (Methods in Molecular Biology; Vol. 1970).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ziebarth, JD, Bhattacharya, A & Cui, Y 2019, Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1970, Humana Press Inc., pp. 101-120. https://doi.org/10.1007/978-1-4939-9207-2_8
Ziebarth JD, Bhattacharya A, Cui Y. Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 101-120. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9207-2_8
Ziebarth, Jesse D. ; Bhattacharya, Anindya ; Cui, Yan. / Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition : Bioinformatics Resources. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 101-120 (Methods in Molecular Biology).
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