Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) to Map Regions of Histone Methylation Patterns in Embryonic Stem Cells

  • Shiliyang Xu
  • Sean Grullon
  • Kai Ge
  • Weiqun Peng
Part of the Methods in Molecular Biology book series (MIMB, volume 1150)


Chromatin states are the key to embryonic stem cell pluripotency and differentiation. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) is increasingly used to map chromatin states and to functionally annotate the genome. Many ChIP-Seq profiles, especially those of histone methylations, are noisy and diffuse. Here we describe SICER (Zang et al., Bioinformatics 25(15):1952–1958, 2009), an algorithm specifically designed to identify disperse ChIP-enriched regions with high sensitivity and specificity. This algorithm has found a lot of applications in epigenomic studies. In this Chapter, we will demonstrate in detail how to run SICER to delineate ChIP-enriched regions and assess their statistical significance, and to identify regions of differential enrichment when two chromatin states are compared.

Key words

ChIP-Seq Histone modifications Epigenetic modifications Epigenome SICER 



This work was supported in part by the Intramural Research Program of the NIDDK, NIH to KG.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Shiliyang Xu
    • 1
    • 3
  • Sean Grullon
    • 1
    • 3
  • Kai Ge
    • 3
  • Weiqun Peng
    • 2
  1. 1.Department of PhysicsThe George Washington UniversityWashingtonUSA
  2. 2.Department of Physics and Department of Anatomy and Regenerative BiologyThe George Washington UniversityWashingtonUSA
  3. 3.Laboratory of Endocrinology and Receptor Biology, Adipocyte Biology and Gene Regulation SectionNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUSA

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