Cargando…

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

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,...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhong, Yi, Karaletsos, Theofanis, Drewe, Philipp, Sreedharan, Vipin T, Kuo, David, Singh, Kamini, Wendel, Hans-Guido, Rätsch, Gunnar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198522/
https://www.ncbi.nlm.nih.gov/pubmed/27634950
http://dx.doi.org/10.1093/bioinformatics/btw585
_version_ 1782488863568035840
author Zhong, Yi
Karaletsos, Theofanis
Drewe, Philipp
Sreedharan, Vipin T
Kuo, David
Singh, Kamini
Wendel, Hans-Guido
Rätsch, Gunnar
author_facet Zhong, Yi
Karaletsos, Theofanis
Drewe, Philipp
Sreedharan, Vipin T
Kuo, David
Singh, Kamini
Wendel, Hans-Guido
Rätsch, Gunnar
author_sort Zhong, Yi
collection PubMed
description 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.
format Online
Article
Text
id pubmed-5198522
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-51985222017-01-06 RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints Zhong, Yi Karaletsos, Theofanis Drewe, Philipp Sreedharan, Vipin T Kuo, David Singh, Kamini Wendel, Hans-Guido Rätsch, Gunnar Bioinformatics Applications Notes 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. Oxford University Press 2017-01-01 2016-09-14 /pmc/articles/PMC5198522/ /pubmed/27634950 http://dx.doi.org/10.1093/bioinformatics/btw585 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Zhong, Yi
Karaletsos, Theofanis
Drewe, Philipp
Sreedharan, Vipin T
Kuo, David
Singh, Kamini
Wendel, Hans-Guido
Rätsch, Gunnar
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
title RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
title_full RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
title_fullStr RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
title_full_unstemmed RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
title_short RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
title_sort ribodiff: detecting changes of mrna translation efficiency from ribosome footprints
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198522/
https://www.ncbi.nlm.nih.gov/pubmed/27634950
http://dx.doi.org/10.1093/bioinformatics/btw585
work_keys_str_mv AT zhongyi ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT karaletsostheofanis ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT drewephilipp ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT sreedharanvipint ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT kuodavid ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT singhkamini ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT wendelhansguido ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints
AT ratschgunnar ribodiffdetectingchangesofmrnatranslationefficiencyfromribosomefootprints