IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity
Abstract
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, e.g., comparing paternal and maternal allele of one individual or comparing tumor and normal sample 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 mouse transcriptome and identify a group of genes whose isoform usages respond to haloperidol treatment.
Keywords
Cite
@article{arxiv.1402.0136,
title = {IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity},
author = {Wei Sun and Yufeng Liu and James J. Crowley and Ting-Huei Chen and Hua Zhou and Haitao Chu and Shunping Huang and Pei-Fen Kuan and Yuan Li and Darla Miller and Ginger Shaw and Yichao Wu and Vasyl Zhabotynsky and Leonard McMillan and Fei Zou and Patrick F. Sullivan and Fernando Pardo-Manuel de Villena},
journal= {arXiv preprint arXiv:1402.0136},
year = {2014}
}