Application of the simple and efficient Mpeak modeling in binding peak identification in ChIP-chip studies.
Application of the simple and efficient Mpeak modeling in binding peak identification in ChIP-chip studies.
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简单高效的 Mpeak 模型在 ChIP 芯片研究中结合峰识别中的应用。
DOI：
10.1007/978-1-62703-607-8_12
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Lau,Yun-FaiChris
中科院分区：
文献类型：
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作者：
Zheng,Ming;Li,Yunmin;Lau,Yun-FaiChris
高密度启动子芯片（ChIP-chip）的染色质免疫沉淀和杂交是在全基因组范围内鉴定特定转录因子和其他dna结合核蛋白靶基因的有力策略。核心设施的服务极大地提高了这些技术对实地新研究人员的可及性。Mpeak建模是一个简单而高效的计算机程序，能够识别ChIP-chip数据集中的染色质结合峰。它利用先进的统计计算，但提供了一个简单的过程，用户输入参数在其操作。mpeak拟合信号以方便的格式制表，可以在各种基因组显示图形程序中可视化，包括SignalMap和Genome Browser，并与其他数据集（如微阵列表达模式）一起分析。几个研究小组在各自的ChIP-chip研究中使用了Mpeak程序。Mpeak的各种特征将通过一项研究的ChIP-chip数据集来说明，该研究旨在确定小鼠胚胎性腺在性别决定时的性别决定因子SRY的靶基因。
Chromatin immunoprecipitation and hybridization of high-density promoter microarray (ChIP-chip) is a powerful strategy to identify target genes for specific transcription factors and other DNA-binding nuclear proteins in a genome-wide manner. Services of core facilities have greatly enhanced the accessibility of these technologies to new investigators to the field. The Mpeak modeling is a simple and efficient computer program, capable of identifying chromatin-binding peaks in ChIP-chip datasets. It utilizes advanced statistical computation, but yet offers a simple procedure with user inputs on parameters in its operation. The Mpeak-fitted signals are tabulation in convenient formats and can be visualized in various genome-display graphic programs, including SignalMap and Genome Browser, and analyzed together with other datasets, such as microarray expression patterns. Several research groups have used the Mpeak program in their respective ChIP-chip studies. The various features of Mpeak will be illustrated with ChIP-chip datasets from a study designed to identify the target genes for the sex-determining factor, SRY, in mouse embryonic gonads at the time of sex determination.