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Streamlining differential exon and 3' UTR usage with diffUTR.

ABSTRACT:

Background

Despite the importance of alternative poly-adenylation and 3' UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data.

Results

We present the diffUTR Bioconductor package which streamlines and improves upon differential exon usage (DEU) analyses, and leverages existing DEU tools and alternative poly-adenylation site databases to enable differential 3' UTR usage analysis. We demonstrate the diffUTR features and show that it is more flexible and more accurate than state-of-the-art alternatives, both in simulations and in real data.

Conclusions

diffUTR enables differential 3' UTR analysis and more generally facilitates DEU and the exploration of their results.

SUBMITTER: Gerber S

PROVIDER: S-EPMC8045333 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Streamlining differential exon and 3' UTR usage with diffUTR.

Gerber Stefan S Schratt Gerhard G Germain Pierre-Luc PL

BMC bioinformatics 20210413 1

<h4>Background</h4>Despite the importance of alternative poly-adenylation and 3' UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data.<h4>Results</h4>We present the diffUTR Bioconductor package which streamlines and improves upon differential exon usage (DEU) analyses, and leverages existing DEU tools and alternative poly-adenylation site databases to enable differential 3' UTR usage analysis. We demonstrate the diff ...[more]

PMID: 33849458

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