RiboDiff: Detecting changes of mRNA translation efficiency from ribosome footprints
OPEN ACCESS
Author / Producer
Date
2017-01
Publication Type
Journal Article
ETH Bibliography
yes
Citations
Altmetric
OPEN ACCESS
Data
Rights / License
Abstract
Motivation
Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case–control studies are needed.
Results
We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy.
Availability and Implementation
RiboDiff webpage http://bioweb.me/ribodiff. Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff.
Supplementary information
Supplementary data are available at Bioinformatics online.
Permanent link
Publication status
published
External links
Editor
Book title
Journal / series
Volume
33 (1)
Pages / Article No.
139 - 141
Publisher
Oxford University Press
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
Organisational unit
09568 - Rätsch, Gunnar / Rätsch, Gunnar
09568 - Rätsch, Gunnar / Rätsch, Gunnar
03957 - Zimmermann, Michael Bruce (emeritus) / Zimmermann, Michael Bruce (emeritus)
Notes
It was possible to publish this article open access thanks to a Swiss National Licence with the publisher.