Gene ontology analysis for RNA-seq: accounting for selection bias

Other free copies

• European Bioinformatics Institute (ncbi.nlm.nih.gov)Preprint · Web page
• The University of Melbourne (hdl.handle.net)Preprint · Web page

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.