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

被引：5505

作者：

Young, Matthew D. ^{[1
]}

Wakefield, Matthew J. ^{[1
]}

Smyth, Gordon K. ^{[1
]}

Oshlack, Alicia ^{[1
]}

机构：

[1] Walter & Eliza Hall Inst Med Res, Bioinformat Div, Parkville, Vic 3052, Australia

来源：

GENOME BIOLOGY | 2010年 / 11卷 / 02期

关键词：

ENRICHMENT ANALYSIS; TOOL;

D O I：

10.1186/gb-2010-11-2-r14

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：12

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