Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints

View ORCID ProfileYi Zhong, View ORCID ProfileTheofanis Karaletsos, View ORCID ProfilePhilipp Drewe, View ORCID ProfileVipin Sreedharan, View ORCID ProfileKamini Singh, View ORCID ProfileHans-Guido Wendel, View ORCID ProfileGunnar Rätsch
doi: https://doi.org/10.1101/017111
Yi Zhong
1Computational Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yi Zhong
Theofanis Karaletsos
1Computational Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Theofanis Karaletsos
Philipp Drewe
2Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Philipp Drewe
Vipin Sreedharan
1Computational Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Vipin Sreedharan
Kamini Singh
3Cancer Biology Program, Sloan Kettering Institute, 1275 York Ave, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kamini Singh
Hans-Guido Wendel
3Cancer Biology Program, Sloan Kettering Institute, 1275 York Ave, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hans-Guido Wendel
Gunnar Rätsch
1Computational Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gunnar Rätsch
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

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 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 Source code and documentation are available at http://github.com/ratschlab/ribodiff. Supplementary Material can be found at http://bioweb.me/ribodiff.

Contact zhongy{at}cbio.mskcc.org and raetsch{at}cbio.mskcc.org.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted March 29, 2015.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints
Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin Sreedharan, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
bioRxiv 017111; doi: https://doi.org/10.1101/017111
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints
Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin Sreedharan, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
bioRxiv 017111; doi: https://doi.org/10.1101/017111

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2440)
  • Biochemistry (4803)
  • Bioengineering (3340)
  • Bioinformatics (14724)
  • Biophysics (6658)
  • Cancer Biology (5188)
  • Cell Biology (7455)
  • Clinical Trials (138)
  • Developmental Biology (4378)
  • Ecology (6904)
  • Epidemiology (2057)
  • Evolutionary Biology (9943)
  • Genetics (7357)
  • Genomics (9550)
  • Immunology (4583)
  • Microbiology (12730)
  • Molecular Biology (4960)
  • Neuroscience (28422)
  • Paleontology (199)
  • Pathology (810)
  • Pharmacology and Toxicology (1400)
  • Physiology (2031)
  • Plant Biology (4521)
  • Scientific Communication and Education (980)
  • Synthetic Biology (1305)
  • Systems Biology (3922)
  • Zoology (731)