Detecting differential usage of exons from RNA-seq data

RNA-seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons between conditions, cell types, or tissues. W...

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Bibliographic Details
Published inGenome research Vol. 22; no. 10; pp. 2008 - 2017
Main Authors Anders, Simon, Reyes, Alejandro, Huber, Wolfgang
Format Journal Article
LanguageEnglish
Published United States Cold Spring Harbor Laboratory Press 01.10.2012
Subjects
Algorithms
Alternative Splicing
Animals
Cell Line
Computational Biology - methods
Databases, Nucleic Acid
Exons
Genomics - methods
Humans
Method
Models, Genetic
Pan troglodytes - genetics
RNA - chemistry
RNA - genetics
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Summary:RNA-seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons between conditions, cell types, or tissues. We present DEXSeq , a statistical method to test for differential exon usage in RNA-seq data. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account. DEXSeq detects with high sensitivity genes, and in many cases exons, that are subject to differential exon usage. We demonstrate the versatility of DEXSeq by applying it to several data sets. The method facilitates the study of regulation and function of alternative exon usage on a genome-wide scale. An implementation of DEXSeq is available as an R/Bioconductor package.
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These authors contributed equally to this work.
ISSN:1088-9051
1549-5469
1549-5469
DOI:10.1101/gr.133744.111