  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.
