Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells

Methods Mol Biol. 2014;1150:97-111. doi: 10.1007/978-1-4939-0512-6_5.


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.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Algorithms*
  • Biostatistics / methods*
  • Chromatin Immunoprecipitation / methods*
  • Cluster Analysis
  • Computational Biology / methods*
  • Embryonic Stem Cells / metabolism*
  • Histones / metabolism*
  • Methylation


  • Histones