title: Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells.
abstract: 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.
authors.affiliation: Department of Physics, The George Washington University, Corcoran Hall, Room 105, 725 21st Street NW, Washington, DC, 20052, USA.
authors.forename: Shiliyang
authors.initials: S
authors.lastname: Xu
authors.forename: Sean
authors.initials: S
authors.lastname: Grullon
authors.forename: Kai
authors.initials: K
authors.lastname: Ge
authors.forename: Weiqun
authors.initials: W
authors.lastname: Peng
mesh_terms: D000465:Algorithms; D056808:Biostatistics / Q000379:methods*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D053595:Embryonic Stem Cells / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D008745:Methylation
chemical_list: D006657:Histones
references.citation: Nat Genet. 2008 Jul;40(7):897-903
references.pmid: 18552846
references.citation: Nature. 2001 Mar 1;410(6824):116-20
references.pmid: 11242053
references.citation: Bioinformatics. 2011 Mar 15;27(6):870-1
references.pmid: 21325299
references.citation: Nature. 2001 Mar 1;410(6824):120-4
references.pmid: 11242054
references.citation: Cell. 2007 May 18;129(4):823-37
references.pmid: 17512414
references.citation: Bioinformatics. 2009 Aug 1;25(15):1952-8
references.pmid: 19505939
references.citation: PLoS Biol. 2011 Apr;9(4):e1001046
references.pmid: 21526222
references.citation: EMBO J. 1999 Apr 1;18(7):1923-38
references.pmid: 10202156
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63
references.pmid: 23193274
references.citation: Neural Comput. 2007 Jun;19(6):1503-27
references.pmid: 17444758
references.citation: Cell. 2009 Sep 4;138(5):1019-31
references.pmid: 19698979
references.citation: EMBO J. 2013 Jan 9;32(1):45-59
references.pmid: 23178591
references.citation: Nat Rev Genet. 2007 Jan;8(1):9-22
references.pmid: 17173055
references.citation: Bioinformatics. 2010 Mar 15;26(6):841-2
references.pmid: 20110278
references.citation: Bioinformatics. 2011 Jan 15;27(2):272-4
references.pmid: 21075741