An effective analytic method for detecting tissue-specific genes in RNA-seq experiments

Guoqing Zhao, Qiao Li, I. Ming Wang, Xiaoqiao Liu, Xiangzhong Fang, Xiaohua Douglas Zhang

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Aim: To develop an analytic method for identifying tissue-specific (TS) genes from RNA-seq data. Materials & 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. Conclusion: Our approach not only directly works on discrete data but also naturally incorporates data variability. It works effectively for detecting TS genes.

Original languageEnglish
Pages (from-to)1769-1779
Number of pages11
JournalPharmacogenomics
Volume16
Issue number16
DOIs
StatePublished - Nov 2015

Bibliographical note

Publisher Copyright:
© 2015 Future Medicine Ltd.

Keywords

  • consecutive procedures
  • generalization of Tukey's test
  • next-generation sequencing
  • RNA-Seq
  • tissue-specific gene

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Pharmacology

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