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Bioinformatics. 2012 Nov 1;28(21):2782-8. doi: 10.1093/bioinformatics/bts515. Epub 2012 Aug 24.

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

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  • 1Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China.

Abstract

MOTIVATION:

RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the gene expression omnibus do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single replicate studies, there is currently no satisfactory method for detecting differentially expressed genes when only a single biological replicate is available. Results: We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold change. In this way, GFOLD overcomes the shortcomings of P-value and fold change calculated by existing RNA-seq analysis methods and gives more stable and biological meaningful gene rankings when only a single biological replicate is available.

AVAILABILITY:

The open source C/C++ program is available at http://www.tongji.edu.cn/∼zhanglab/GFOLD/index.html

PMID:
22923299
[PubMed - indexed for MEDLINE]
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