Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching.

ABSTRACT: Switching between different alternative polyadenylation (APA) sites plays an important role in the fine tuning of gene expression. New technologies for the execution of 3'-end enriched RNA-seq allow genome-wide detection of the genes that exhibit significant APA site switching between different samples. Here, we show that the independence test gives better results than the linear trend test in detecting APA site-switching events. Further examination suggests that the discrepancy between these two statistical methods arises from complex APA site-switching events that cannot be represented by a simple change of average 3'-UTR length. In theory, the linear trend test is only effective in detecting these simple changes. We classify the switching events into four switching patterns: two simple

SUBMITTER: Li J 

PROVIDER: S-EPMC4396989 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature