Gene ontology analysis for RNA-seq: accounting for selection bias.
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ABSTRACT:
SUBMITTER: Young MD
PROVIDER: S-EPMC2872874 | biostudies-literature | 2010
REPOSITORIES: biostudies-literature
Publications
Gene ontology analysis for RNA-seq: accounting for selection bias.
Young Matthew D MD Wakefield Matthew J MJ Smyth Gordon K GK Oshlack Alicia A
Genome biology 20100204 2
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 consisten ...[more]
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