Evaluation of Bioinformatics Approaches for Next-Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design

Frontiers in Genetics
Halil BisginWeida Tong

Abstract

MicroRNAs (miRNAs) are key post-transcriptional regulators that affect protein translation by targeting mRNAs. Their role in disease etiology and toxicity are well recognized. Given the rapid advancement of next-generation sequencing techniques, miRNA profiling has been increasingly conducted with RNA-seq, namely miRNA-seq. Analysis of miRNA-seq data requires several steps: (1) mapping the reads to miRBase, (2) considering mismatches during the hairpin alignment (windowing), and (3) counting the reads (quantification). The choice made in each step with respect to the parameter settings could affect miRNA quantification, differentially expressed miRNAs (DEMs) detection and novel miRNA identification. Furthermore, these parameters do not act in isolation and their joint effects impact miRNA-seq results and interpretation. In toxicogenomics, the variation associated with parameter setting should not overpower the treatment effect (such as the dose/time-dependent effect). In this study, four commonly used miRNA-seq analysis tools (i.e., miRDeep2, miRExpress, miRNAkey, sRNAbench) were comparatively evaluated with a standard toxicogenomics study design. We tested 30 different parameter settings on miRNA-seq data generated from thioac...Continue Reading

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Citations

Feb 23, 2020·The FEBS Journal·Alexander E Vinogradov, Olga V Anatskaya
Sep 3, 2020·Biomolecules·Adrian Garcia-Moreno, Pedro Carmona-Saez
Aug 20, 2020·Reviews in the Neurosciences·Barbora KonečnáGabriela Repiská
Apr 1, 2021·Cellular Signalling·Mridul BudakotiManisha Nigam
Apr 16, 2021·Applications in Plant Sciences·Qinglian LiQi You
Jun 17, 2021·Molecular Medicine Reports·Qi Zheng, Wei Hou

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Methods Mentioned

BETA
RNA-seq
miRNA-seq

Software Mentioned

MIReNA
miRDeep2
miRanalyzer
miRNAKey
mirTools
FASTX
Bowtie
sRNAbench
EM
WinDown

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