title: GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The open source C/C++ program is available at http://www.tongji.edu.cn/∼zhanglab/GFOLD/index.html
authors.affiliation: Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China.
authors.forename: Jianxing
authors.initials: J
authors.lastname: Feng
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: X
authors.initials: X
authors.lastname: Shirley Liu
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012313:RNA / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000191:economics / Q000379:methods*
chemical_list: D012313:RNA