[HTML][HTML] Gene ontology analysis for RNA-seq: accounting for selection bias

MD Young, MJ Wakefield, GK Smyth, A Oshlack - Genome biology, 2010 - Springer
Genome biology, 2010Springer
We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq
data. GO analysis is widely used to reduce complexity and highlight biological processes in
genome-wide expression studies, but standard methods give biased results on RNA-seq
data due to over-detection of differential expression for long and highly expressed
transcripts. Application of GOseq to a prostate cancer data set shows that GOseq
dramatically changes the results, highlighting categories more consistent with the known …
Abstract
We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.
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