title: An effective analytic method for detecting tissue-specific genes in RNA-seq experiments.
abstract: OBJECTIVE
  To develop an analytic method for identifying tissue-specific (TS) genes from RNA-seq data.
  
  
  METHODS
  Based on a negative binomial distribution, we develop a statistical method containing consecutive procedures incorporating data variability from replicates in each tissue.
  
  
  RESULTS
  Simulations show that our approach can effectively identify at least 94% of the truly TS genes if the sample size is 3 and at least 84% of the TS genes detected by our method are truly TS genes. We illustrated the utility of our method in an in-house RNA-seq project and produced sensible results.
  
  
  CONCLUSIONS
  Our approach not only directly works on discrete data but also naturally incorporates data variability. It works effectively for detecting TS genes.
authors.affiliation: School of Mathematical Sciences, Peking University, Beijing 100871, China.|BARDS,MSD R&D (China), Beijing 100015, China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Zhao
authors.affiliation: BARDS,MSD R&D (China), Beijing 100015, China.
authors.forename: Qiao
authors.initials: Q
authors.lastname: Li
authors.affiliation: Discovery Pharmacogenomics, Merck Research Laboratories, West Point, PA 19486, USA.
authors.forename: I-Ming
authors.initials: IM
authors.lastname: Wang
authors.affiliation: Scientific Informatics, MSD R&D (China), Beijing 100015, China.
authors.forename: Xiaoqiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Mathematical Sciences, Peking University, Beijing 100871, China.
authors.forename: Xiangzhong
authors.initials: X
authors.lastname: Fang
authors.affiliation: Biometrics Research, Merck Research Laboratories, West Point, PA 19486, USA.
authors.forename: Xiaohua Douglas
authors.initials: XD
authors.lastname: Zhang
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008957:Models, Genetic; D009928:Organ Specificity / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
keywords: RNA-Seq; consecutive procedures; generalization of Tukey's test; next-generation sequencing; tissue-specific gene