用于识别芯片富集区域（SICER）的空间聚类，以绘制胚胎干细胞中组蛋白甲基化模式的区域。
Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells.
作者信息
Xu Shiliyang, Grullon Sean, Ge Kai, Peng Weiqun
机构信息
Department of Physics, The George Washington University, Corcoran Hall, Room 105, 725 21st Street NW, Washington, DC, 20052, USA.
出版信息
Methods Mol Biol. 2014;1150:97-111. doi: 10.1007/978-1-4939-0512-6_5.
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.
摘要
染色质状态是胚胎干细胞多能性和分化的关键。染色质免疫沉淀（ChIP）结合高通量测序（ChIP-Seq）越来越多地用于绘制染色质状态并对基因组进行功能注释。许多ChIP-Seq图谱，尤其是组蛋白甲基化的图谱，都存在噪声且分散。在此我们描述SICER（Zang等人，《生物信息学》25(15):1952 - 1958，2009年），这是一种专门设计用于以高灵敏度和特异性识别分散的ChIP富集区域的算法。该算法已在表观基因组学研究中得到广泛应用。在本章中，我们将详细演示如何运行SICER来描绘ChIP富集区域并评估其统计显著性，以及在比较两种染色质状态时识别差异富集区域。
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本文引用的文献
1
ENCODE data in the UCSC Genome Browser: year 5 update.在 UCSC 基因组浏览器中编码数据：第 5 年更新。
Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. doi: 10.1093/nar/gks1172. Epub 2012 Nov 27.
2
Histone H3K9 methyltransferase G9a represses PPARγ expression and adipogenesis.组蛋白 H3K9 甲基转移酶 G9a 抑制 PPARγ 的表达和脂肪生成。
EMBO J. 2013 Jan 9;32(1):45-59. doi: 10.1038/emboj.2012.306. Epub 2012 Nov 23.
3
A user's guide to the encyclopedia of DNA elements (ENCODE).DNA 元件百科全书（ENCODE）使用指南
PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.
4
Identifying dispersed epigenomic domains from ChIP-Seq data.从 ChIP-Seq 数据中识别离散的表观基因组域。
Bioinformatics. 2011 Mar 15;27(6):870-1. doi: 10.1093/bioinformatics/btr030. Epub 2011 Feb 16.
5
The uniqueome: a mappability resource for short-tag sequencing.独特组学：短标签测序的可作图资源。
Bioinformatics. 2011 Jan 15;27(2):272-4. doi: 10.1093/bioinformatics/btq640. Epub 2010 Nov 12.
6
BEDTools: a flexible suite of utilities for comparing genomic features.BEDTools：一套灵活的基因组特征比较工具套件。
Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.
7
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes.全基因组范围内对组蛋白乙酰转移酶（HATs）和组蛋白去乙酰化酶（HDACs）的图谱绘制揭示了它们在活跃基因和非活跃基因中的不同功能。
Cell. 2009 Sep 4;138(5):1019-31. doi: 10.1016/j.cell.2009.06.049. Epub 2009 Aug 20.
8
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.一种基于聚类的方法，用于从组蛋白修饰 ChIP-Seq 数据中识别富集结构域。
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9
Combinatorial patterns of histone acetylations and methylations in the human genome.人类基因组中组蛋白乙酰化和甲基化的组合模式。
Nat Genet. 2008 Jul;40(7):897-903. doi: 10.1038/ng.154. Epub 2008 Jun 15.
10
High-resolution profiling of histone methylations in the human genome.人类基因组中组蛋白甲基化的高分辨率分析。
Cell. 2007 May 18;129(4):823-37. doi: 10.1016/j.cell.2007.05.009.
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