Gene Ontology Analysis for RNA-seq: Accounting for Selection Bias

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2010 Feb 6

PMID 20132535

Citations 3226

Authors

Matthew D Young

Matthew J Wakefield

Gordon K Smyth

Alicia Oshlack

Affiliations

Soon will be listed here.

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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