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

Genome Biol. 2010;11(2):R14. doi: 10.1186/gb-2010-11-2-r14. Epub 2010 Feb 4.


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.

MeSH terms

  • Androgens / pharmacology
  • Bias
  • Cell Line, Tumor
  • Gene Expression Regulation, Neoplastic
  • Genome-Wide Association Study
  • Humans
  • Male
  • Prostatic Neoplasms / genetics*
  • Sequence Analysis, RNA / methods*


  • Androgens