Gerber S, Schratt G, Germain PL. Streamlining differential exon and 3' UTR usage with diffUTR.
BMC Bioinformatics 2021;
22:189. [PMID:
33849458 PMCID:
PMC8045333 DOI:
10.1186/s12859-021-04114-7]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
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.
Supplementary Information
The online version contains supplementary material available at 10.1186/s12859-021-04114-7.
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