RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

• Published in: Bioinformatics (Oxford, England) Vol. 33; no. 1; pp. 139 - 141
• Main Authors: Zhong, Yi, Karaletsos, Theofanis, Drewe, Philipp, Sreedharan, Vipin T, Kuo, David, Singh, Kamini, Wendel, Hans-Guido, Rätsch, Gunnar
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2017
• Subjects: Applications Notes; Gene Expression Regulation; High-Throughput Nucleotide Sequencing - methods; Protein Biosynthesis; Ribosomes - metabolism; RNA, Messenger - metabolism; Sequence Analysis, RNA - methods; Software
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btw585

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. 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. RiboDiff webpage http://bioweb.me/ribodiff Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff CONTACTS: zhongy@cbio.mskcc.org or raetsch@inf.ethz.chSupplementary information: Supplementary data are available at Bioinformatics online.