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Genome Biol. 2010;11(2):R14. Epub 2010 Feb 4.

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

Young MD, Wakefield MJ, Smyth GK, Oshlack A.

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Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3052, Australia.

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.

PMID:: 20132535; [PubMed - indexed for MEDLINE]
PMCID:: PMC2872874

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