Chromatin-state discovery and genome annotation with ChromHMM.

Chromatin-state discovery and genome annotation with ChromHMM.
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DOI:
10.1038/nprot.2017.124
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发表时间:
2017-12
期刊:
影响因子:
14.8
通讯作者:
Kellis M
Kellis M
中科院分区:
生物学1区
文献类型:
--
作者:
Ernst J;Kellis M

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非编码DNA区域在人类生物学、进化和疾病中起着核心作用。ChromHMM使用一种或多种细胞类型的表观基因组信息帮助注释非编码基因组。它结合了多个全基因组表观基因组图谱,并使用组合和空间标记模式来推断每种细胞类型的完整注释。ChromHMM使用多变量隐马尔可夫模型学习染色质状态签名,该模型明确地对每个标记的组合存在或不存在进行建模。ChromHMM通过计算每个基因组片段中最可能的状态,使用这些签名为每个细胞类型生成全基因组注释。ChromHMM提供了对所得到的注释的自动富集分析,以促进对每个染色质状态的功能解释。ChromHMM的特点在于其对标记组合的建模强调,与下游功能富集分析的紧密集成,速度快,易于使用。一天之内即可学习染色质状态、生成注释并计算富集度。
Non-coding DNA regions play central roles in human biology, evolution, and disease. ChromHMM helps annotate the non-coding genome using epigenomic information across one or multiple cell types. It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type. ChromHMM learns chromatin state signatures using a multivariate hidden Markov model that explicitly models the combinatorial presence or absence of each mark. ChromHMM uses these signatures to generate a genome-wide annotation for each cell type, by calculating the most probable state in each genomic segment. ChromHMM provides automated enrichment analysis of the resulting annotations to facilitate the functional interpretations of each chromatin state. ChromHMM is distinguished by its modeling emphasis on combinations of marks, its tight integration with downstream functional enrichment analyses, its speed, and its ease of use. Chromatin states are learned, annotations produced, and enrichments computed within one day.
DOI: 10.1038/nature09906
发表时间: 2011-05-05
期刊: NATURE
影响因子: 64.8
作者:
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
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DOI: 10.1038/nbt.3157
发表时间: 2015-04
影响因子: 46.9
作者:
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发表时间: 2012-09
期刊: Genome research
影响因子: 7
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发表时间: 2014-07-01
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影响因子: 7
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