Design and analysis of ChIP-seq experiments for DNA-binding proteins.
Design and analysis of ChIP-seq experiments for DNA-binding proteins.
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DOI：
10.1038/nbt.1508
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发表时间：
2008-12
影响因子：
46.9
通讯作者：
Park, Peter J.
中科院分区：
文献类型：
--
作者：
Kharchenko, Peter V.;Tolstorukov, Michael Y.;Park, Peter J.
大规模并行测序平台的最新进展使人们能够使用染色质免疫沉淀和测序(CHIP-SEQ)相结合的方法对DNA相关蛋白质进行全基因组测量。虽然存在用于分析已建立的微阵列替代物(芯片-芯片)的各种方法，但很少描述用于处理芯片序列数据的方法。为了填补这一空白，我们提出了一种专门设计的分析管道，以高精度检测蛋白质结合位置。使用三个独立的数据集，我们说明了改进标签对齐和校正背景信号的新方法。我们还比较了几种新的和先前描述的结合检测算法的灵敏度和空间精度。最后，我们分析了测序深度与检测到的结合部位特征之间的关系，并提供了一种估计所需蛋白质结合部位覆盖所需测序深度的方法。
Recent progress in massively parallel sequencing platforms has allowed for genome-wide measurements of DNA-associated proteins using a combination of chromatin immunoprecipitation and sequencing (ChIP-seq). While a variety of methods exist for analysis of the established microarray alternative (ChIP-chip), few approaches have been described for processing ChIP-seq data. To fill this gap, we propose an analysis pipeline specifically designed to detect protein binding positions with high accuracy. Using three separate datasets, we illustrate new methods for improving tag alignment and correcting for background signals. We also compare sensitivity and spatial precision of several novel and previously described binding detection algorithms. Finally, we analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.
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