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

Methods in Molecular Biology

Volumn 1150, Issue , 2014, Pages 97-111

  Xu, Shiliyang ^a   Grullon, Sean ^a   Ge, Kai ^a   Peng, Weiqun ^a  

^a NONE

Author keywords

ChIP Seq; Epigenetic modifications; Epigenome; Histone modifications; SICER

Indexed keywords

ALGORITHM; ANIMAL CELL; ARTICLE; BIOINFORMATICS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EMBRYONIC STEM CELL; EPIGENETICS; HIGH THROUGHPUT SEQUENCING; HISTONE METHYLATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SPATIAL CLUSTERING FOR IDENTIFICATION OF CHROMATIN IMMUNOPRECIPITATION ENRICHED REGION; BIOLOGY; BIOSTATISTICS; CLUSTER ANALYSIS; METABOLISM; METHYLATION; PROCEDURES;

HISTONE;

ALGORITHMS; BIOSTATISTICS; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EMBRYONIC STEM CELLS; HISTONES; METHYLATION;

EID: 84921425052     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0512-6_5     Document Type: Article

References (16)

1. Barski A, Cuddapah S, Cui KR, Roh TY, Schones DE, Wang ZB, Wei G, Chepelev I, Zhao KJ (2007) High-resolution profiling of histone methylations in the human genome. Cell 129(4):823–837
2. Wang ZB, Zang CZ, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui KR, Roh TY, Peng WQ, Zhang MQ, Zhao KJ (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40(7):897–903
3. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138(5):1019–1031
4. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25(15):1952–1958
5. Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, Schotta G, Kuhfittig S, Wolf A, Lebersorger A, Singh PB, Reuter G, Jenuwein T (1999) Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J 18(7): 1923–1938
6. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410(6824): 120–124
7. Lachner M, O’Carroll N, Rea S, Mechtler K, Jenuwein T (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410(6824):116–120
8. Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8(1):9–22
9. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57:289–300
10. Shimazaki H, Shinomoto S (2007) A method for selecting the bin size of a time histogram. Neural Comput 19:1503–1527
11. Song Q, Smith AD (2011) Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27(6):870–871. doi:10.1093/ bioinformatics/btr030
12. Koehler R, Issac H, Cloonan N, Grimmond SM (2010) The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics. doi:10.1093/bioinformatics/btq640
13. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842. doi:10.1093/bioinformatics/btq033
14. The EPC (2011) A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9(4):e1001046. doi:10.1371/journal. pbio.1001046
15. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ (2012) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. doi:10.1093/nar/ gks1172
16. Wang L, Xu S, Lee J-E, Baldridge A, Grullon S, Peng W, Ge K (2013) Histone H3K9 methyltransferase G9a represses PPAR[gamma] expression and adipogenesis. EMBO J 32(1):45–59. http://www.nature.com/emboj/journal/ v32/n1/suppinfo/emboj2012306a_S1.html