Identifying differential transcription factor binding in ChIP-seq.

ABSTRACT: ChIP seq is a widely used assay to measure genome-wide protein binding. The decrease in costs associated with sequencing has led to a rise in the number of studies that investigate protein binding across treatment conditions or cell lines. In addition to the identification of binding sites, new studies evaluate the variation in protein binding between conditions. A number of approaches to study differential transcription factor binding have recently been developed. Several of these methods build upon established methods from RNA-seq to quantify differences in read counts. We compare how these new approaches perform on different data sets from the ENCODE project to illustrate the impact of data processing pipelines under different study designs. The performance of normalization methods for

SUBMITTER: Wu DY 

PROVIDER: S-EPMC4413818 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature