RiboDiff: Detecting changes of mRNA translation efficiency from ribosome footprints

Yi Zhong; Theofanis Karaletsos; Philipp Drewe; Vipin T. Sreedharan; David Kuo; Kamini Singh; Hans Guido Wendel; Gunnar Rätsch

doi:10.1093/bioinformatics/btw585

RiboDiff: Detecting changes of mRNA translation efficiency from ribosome footprints

Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans Guido Wendel, Gunnar Rätsch

Research output: Contribution to journal › Article › peer-review

94 Scopus citations

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.

Original language	English (US)
Pages (from-to)	139-141
Number of pages	3
Journal	Bioinformatics
Volume	33
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/btw585
State	Published - Jan 1 2017
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btw585

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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.",

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doi = "10.1093/bioinformatics/btw585",

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AU - Zhong, Yi

AU - Karaletsos, Theofanis

AU - Drewe, Philipp

AU - Sreedharan, Vipin T.

AU - Kuo, David

AU - Singh, Kamini

AU - Wendel, Hans Guido

AU - Rätsch, Gunnar

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RiboDiff: Detecting changes of mRNA translation efficiency from ribosome footprints

Abstract

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