BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.

ABSTRACT:

Background

Unraveling transcriptional regulatory networks is a central problem in molecular biology and, in this quest, chromatin immunoprecipitation and sequencing (ChIP-seq) technology has given us the unprecedented ability to identify sites of protein-DNA binding and histone modification genome wide. However, multiple systemic and procedural biases hinder harnessing the full potential of this technology. Previous studies have addressed this problem, but a thorough characterization of different, interacting biases on ChIP-seq signals is still lacking.

Results

Here, we present a novel framework where the genome-wide ChIP-seq signal is viewed as being quantifiably influenced by different, measurable sources of bias, which can then be computationally subtracted away. We use a

SUBMITTER: Ramachandran P 

PROVIDER: S-EPMC4574076 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature