Detecting differential usage of exons from RNA-seq data

作者：Anders, Simon^*; Reyes, Alejandro; Huber, Wolfgang

来源：Genome Research, 2012, 22(10): 2008-2017.

DOI：10.1101/gr.133744.111

• EXPRESSION ANALYSIS
• SAGE
• QUANTIFICATION
• BIOCONDUCTOR
• TRANSCRIPTS
• ACTIVATION

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.

• 出版日期2012-10