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

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Creator
  • Starmer, Joshua D
    • Affiliation: School of Medicine, Department of Genetics, N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
  • Magnuson, Terry
    • Affiliation: School of Medicine, Department of Genetics, N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
Abstract
  • 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.
Date of publication
Identifier
  • doi:10.1186/s12859-016-0991-z
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Starmer and Magnuson.
Language
  • English
Bibliographic citation
  • BMC Bioinformatics. 2016 Mar 24;17(1):144
Publisher
  • BioMed Central
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