Stefan Gerber1,2, Gerhard Schratt2, Pierre-Luc Germain3,4,5. 1. Group of Computational Neurogenomics, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. 2. Lab of Systems Neuroscience, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. 3. Group of Computational Neurogenomics, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. pierre-luc.germain@hest.ethz.ch. 4. Lab of Statistical Bioinformatics, DMLS, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. pierre-luc.germain@hest.ethz.ch. 5. SIB Swiss Institute of Bioinformatics, Zurich, Switzerland. pierre-luc.germain@hest.ethz.ch.
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.
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.
Entities:
Keywords:
Alternative poly-adenylation; Alternative splicing; Differential exon usage; Gene expression; RNAseq; Transcriptomic; UTR; Untranslated region
Authors: Adnan Derti; Philip Garrett-Engele; Kenzie D Macisaac; Richard C Stevens; Shreedharan Sriram; Ronghua Chen; Carol A Rohl; Jason M Johnson; Tomas Babak Journal: Genome Res Date: 2012-03-27 Impact factor: 9.043
Authors: Lei Li; Chabane Tibiche; Cong Fu; Tomonori Kaneko; Michael F Moran; Martin R Schiller; Shawn Shun-Cheng Li; Edwin Wang Journal: Genome Res Date: 2011-12-22 Impact factor: 9.043