Accurate detection of differential RNA processing
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Philipp Drewe
- Oliver Stegle
- Lisa Hartmann
- Andre Kahles
- Regina Bohnert
- Andreas Wachter
- Karsten Borgwardt
- Gunnar Raetsch
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000319806600013&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/nar/gkt211
- eISSN
- 1362-4962
- Externe Identifier
- Clarivate Analytics Document Solution ID: 156FG
- PubMed Identifier: 23585274
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- 10
- Zeitschrift
- NUCLEIC ACIDS RESEARCH
- Paginierung
- 5189 - 5198
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Titel
- Accurate detection of differential RNA processing
- Sub types
- Article
- Ausgabe der Zeitschrift
- 41
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Philipp Drewe
- Oliver Stegle
- Lisa Hartmann
- André Kahles
- Regina Bohnert
- Andreas Wachter
- Karsten Borgwardt
- Gunnar Rätsch
- DOI
- 10.1093/nar/gkt211
- eISSN
- 1362-4962
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- 10
- Zeitschrift
- Nucleic Acids Research
- Sprache
- en
- Online publication date
- 2013
- Paginierung
- 5189 - 5198
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/nar/gkt211
- Datum der Datenerfassung
- 2024
- Titel
- Accurate detection of differential RNA processing
- Ausgabe der Zeitschrift
- 41
Datenquelle: Crossref
- Abstract
- Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT-qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation.
- Addresses
- Computational Biology Center, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10065, USA. drewe@cbio.mskcc.org
- Autoren
- Philipp Drewe
- Oliver Stegle
- Lisa Hartmann
- André Kahles
- Regina Bohnert
- Andreas Wachter
- Karsten Borgwardt
- Gunnar Rätsch
- DOI
- 10.1093/nar/gkt211
- eISSN
- 1362-4962
- Externe Identifier
- PubMed Identifier: 23585274
- PubMed Central ID: PMC3664801
- Funding acknowledgements
- NCI NIH HHS: U24 CA143840
- Open access
- true
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- 10
- Zeitschrift
- Nucleic acids research
- Schlüsselwörter
- Animals
- Drosophila melanogaster
- Arabidopsis
- Data Interpretation, Statistical
- Gene Expression Profiling
- Reverse Transcriptase Polymerase Chain Reaction
- RNA Processing, Post-Transcriptional
- Algorithms
- Molecular Sequence Annotation
- RNA Isoforms
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2013
- Open access status
- Open Access
- Paginierung
- 5189 - 5198
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Publisher licence
- CC BY-NC
- Datum der Datenerfassung
- 2013
- Titel
- Accurate detection of differential RNA processing.
- Sub types
- Research Support, Non-U.S. Gov't
- research-article
- Validation Study
- Journal Article
- Research Support, N.I.H., Extramural
- Ausgabe der Zeitschrift
- 41
Files
https://academic.oup.com/nar/article-pdf/41/10/5189/25363621/gkt211.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23585274/pdf/?tool=EBI https://europepmc.org/articles/PMC3664801?pdf=render
Datenquelle: Europe PubMed Central
- Abstract
- Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT-qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation.
- Autoren
- Philipp Drewe
- Oliver Stegle
- Lisa Hartmann
- André Kahles
- Regina Bohnert
- Andreas Wachter
- Karsten Borgwardt
- Gunnar Rätsch
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/23585274
- DOI
- 10.1093/nar/gkt211
- eISSN
- 1362-4962
- Externe Identifier
- PubMed Central ID: PMC3664801
- Funding acknowledgements
- NCI NIH HHS: U24 CA143840
- Ausgabe der Veröffentlichung
- 10
- Zeitschrift
- Nucleic Acids Res
- Schlüsselwörter
- Algorithms
- Animals
- Arabidopsis
- Data Interpretation, Statistical
- Drosophila melanogaster
- Gene Expression Profiling
- Molecular Sequence Annotation
- RNA Isoforms
- RNA Processing, Post-Transcriptional
- Reverse Transcriptase Polymerase Chain Reaction
- Sprache
- eng
- Country
- England
- Paginierung
- 5189 - 5198
- PII
- gkt211
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2013
- Titel
- Accurate detection of differential RNA processing.
- Sub types
- Journal Article
- Research Support, N.I.H., Extramural
- Research Support, Non-U.S. Gov't
- Validation Study
- Ausgabe der Zeitschrift
- 41
Datenquelle: PubMed
- Beziehungen:
- Eigentum von