IsoDOT Detects Differential RNA-Isoform Expression/Usage With Respect to a Categorical or Continuous Covariate With High Sensitivity and Specificity
成果类型：
Article
署名作者：
Sun, Wei; Liu, Yufeng; Crowley, James J.; Chen, Ting-Huei; Zhou, Hua; Chu, Haitao; Huang, Shunping; Kuan, Pei-Fen; Li, Yuan; Miller, Darla; Shaw, Ginger; Wu, Yichao; Zhabotynsky, Vasyl; McMillan, Leonard; Zou, Fei; Sullivan, Patrick F.; de Villena, Fernando Pardo-Manuel
署名单位：
University of North Carolina; University of North Carolina Chapel Hill; University of North Carolina; University of North Carolina Chapel Hill; University of North Carolina; University of North Carolina Chapel Hill; North Carolina State University; University of Minnesota System; University of Minnesota Twin Cities; University of North Carolina; University of North Carolina Chapel Hill
刊物名称：
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
ISSN/ISSBN：
0162-1459
DOI：
10.1080/01621459.2015.1040880
发表日期：
2015
页码：
975-986
关键词：
seq data
gene
quantification
transcriptome
landscape
selection
snap-25
MODEL
Lasso
tool
摘要：
We have developed a statistical method named IsoDOT to assess differential isoform expression (DIE) and differential isoform usage (DIU) using RNA-seq data. Here isoform usage refers to relative isoform expression given the total expression of the corresponding gene. IsoDOT performs two tasks that cannot be accomplished by existing methods: to test DIE/DIU with respect to a continuous covariate, and to test DIE/DIU for one case versus one control. The latter task is not an uncommon situation in practice, for example, comparing the paternal and maternal alleles of one individual or comparing tumor and normal samples of one cancer patient. Simulation studies demonstrate the high sensitivity and specificity of IsoDOT. We apply IsoDOT to study the effects of haloperidol treatment on the mouse transcriptome and identify a group of genes whose isoform usages respond to haloperidol treatment. Supplementary materials for this article are available online.