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RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

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Item Type:Article
Title:RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Creators Name:Zhong, Y. and Karaletsos, T. and Drewe, P. and Sreedharan, V.T. and Kuo, D. and Singh, K. and Wendel, H.G. and Raetsch, G.
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.
Keywords:Gene Expression Regulation, High-Throughput Nucleotide Sequencing, Messenger RNA, Protein Biosynthesis, Ribosomes, RNA Sequence Analysis, Software
Source:Bioinformatics
ISSN:1367-4803
Publisher:Oxford University Press (U.K.)
Volume:33
Number:1
Page Range:139-141
Date:1 January 2017
Additional Information:AVAILABILITY: RiboDiff webpage http://bioweb.me/ribodiff Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff CONTACT: zhongy@cbio.mskcc.org and gunnar@ratschlab.org.
Official Publication:https://doi.org/10.1093/bioinformatics/btw585
PubMed:View item in PubMed
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http://edoc.mdc-berlin.de/16876/Preprint version

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