Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.

ABSTRACT:

Background

Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each one. Datasets that span these two categories are often analyzed with a single program for peak calling combined with an ad hoc method for domains.

Results

We developed hiddenDomains, which identifies both peaks and domains, and compare it to the leading algorithms using H3K27me3, H3K36me3, GABP, ESR1 and FOXA ChIP-seq datasets. The output from the programs was compared to qPCR-validated enriched and depleted sites, predicted transcription factor binding sites,

SUBMITTER: Starmer J 

PROVIDER: S-EPMC4806451 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature