Gene ontology analysis for RNA-seq: accounting for selection bias
- Author(s)
- Young, MD; Wakefield, MJ; Smyth, GK; Oshlack, A;
- Details
- Publication Year 2010,Volume 11,Issue #2,Page R14
- Journal Title
- GENOME BIOLOGY
- Publication Type
- Journal Article
- 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.
- Publisher
- BIOMED CENTRAL LTD
- Keywords
- ENRICHMENT ANALYSIS; PROSTATE-CANCER; BIOLOGY; GENOME; BRAIN; TOOL
- Research Division(s)
- Bioinformatics
- Publisher's Version
- https://doi.org/10.1186/gb-2010-11-2-r14
- Open Access at Publisher's Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872874/- Terms of Use/Rights Notice
- © 2010 Young et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Creation Date: 2010-01-01 12:00:00