title: 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, and highly-transcribed gene bodies. With every method, hiddenDomains, performed as well as, if not better than algorithms dedicated to a specific type of analysis.
  
  
  CONCLUSIONS
  hiddenDomains performs as well as the best domain and peak calling algorithms, making it ideal for analyzing ChIP-seq datasets, especially those that contain a mixture of peaks and domains.
authors.affiliation: Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. starmer@unc.edu.|Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. starmer@unc.edu.
authors.forename: Joshua
authors.initials: J
authors.lastname: Starmer
authors.affiliation: Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.|Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
authors.forename: Terry
authors.initials: T
authors.lastname: Magnuson
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation; D047628:Estrogen Receptor alpha / Q000378:metabolism; D051268:GA-Binding Protein Transcription Factor / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D008390:Markov Chains
chemical_list: D047628:Estrogen Receptor alpha; D051268:GA-Binding Protein Transcription Factor; D006657:Histones
keywords: ChIP-seq; Computational analysis; Histone modifications; hiddenDomains