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

Genome Biology
Matthew D YoungAlicia Oshlack

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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Citations

Nov 17, 2011·Applied Microbiology and Biotechnology·Tiezheng YuanBin Yao
Aug 17, 2011·Environmental Science & Technology·Rute F DomingosKevin J Wilkinson
Dec 31, 2010·Nature Reviews. Genetics·Fatih Ozsolak, Patrice M Milos
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Mar 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·Yuval ItanJean-Laurent Casanova
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Jun 5, 2013·Bioinformatics·Paul GeeleherCathal Seoighe
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Jul 20, 2012·BMC Systems Biology·Zhongxue ChenYouping Deng

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

GSEA
GOToolBox
Bowtie
DAVID
GOseq
GOminer
EasyGO
topGO
mgcv
BiasedUrn

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