Comparing change-point locations of independent profiles with application to gene annotation

TL;DR

This paper develops methods to compare change-point locations in gene expression profiles from different conditions, revealing differential splicing in UTR boundaries and conserved intron boundaries, with applications to yeast RNA-Seq data.

Contribution

It introduces two new methods for comparing change-points in independent profiles, extending existing frameworks to assess differential splicing.

Findings

UTR boundaries show differential splicing across conditions

Intron boundaries are conserved in all profiles

Methods are implemented in an R package EBS available on CRAN

Abstract

We are interested in the comparison of transcript boundaries from cells which originated in different environments. The goal is to assess whether this phenomenon, called differential splicing, is used to modify the transcription of the genome in response to stress factors. We address this question by comparing the change-points locations in the individual segmentation of each profile, which correspond to the RNA-Seq data for a gene in one growth condition. This requires the ability to evaluate the uncertainty of the change-point positions, and the work of Rigaill et. al. (2011) provides an appropriate framework in such case. Building on their approach, we propose two methods for the comparison of change-points, and illustrate our results on a dataset from the yeast specie. We show that the UTR boundaries are subject to differential splicing, while the intron boundaries are conserved in all profiles. Our approach is implemented in an R package called EBS which is available on the CRAN.