Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.
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DOI：
10.1186/1471-2105-9-523
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发表时间：
2008-12-05
影响因子：
3
通讯作者：
Boucher KM
中科院分区：
文献类型：
--
作者：
Nix DA;Courdy SJ;Boucher KM
高吞吐量的签名测序有许多诺言，其中之一是体内转录因子结合位点的现成鉴定，组蛋白的修饰，染色质结构的变化以及在这些实验中的DNA甲基化的模式，用于染色质免疫沉淀。特定的DNA序列和签名测序用于将区域映射到基因组（CHIP-SEQ）。 DNA蛋白结合/修饰提供了重建基因调节网络和染色质重塑的网络，直接发育，对细胞扰动的反应以及肿瘤转化。
在这里，我们提出了使用控制输入数据的算法和软件，以减少误报，并使用两个模拟的SPIKE-IN数据集比较了几种不同的方法。差异得分的差异是5％的错误发现率（FDR）的回收率的两倍以上。发现经验FDR可以预测2-3倍的真实FDR，并且比全局泊松P值更可靠地估计了置信度。 CHIP-SEQ数据不依赖广泛的QPCR验证的NRSF位点以及用于设置阈值的NRSF结合基序的存在。
在这里开发和测试的方法显示出较大的希望，即减少假阳性并估算Chip-seq数据的信心，而没有任何事先了解芯片目标的一部分。网/。
High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications, changes in chromatin structure and patterns of DNA methylation across entire genomes. In these experiments, chromatin immunoprecipitation is used to enrich for particular DNA sequences of interest and signature sequencing is used to map the regions to the genome (ChIP-Seq). Elucidation of these sites of DNA-protein binding/modification are proving instrumental in reconstructing networks of gene regulation and chromatin remodelling that direct development, response to cellular perturbation, and neoplastic transformation. Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized difference score were found to more than double the recovery of ChIP-Seq peaks at a 5% false discovery rate (FDR). Moreover, both a binomial p-value/q-value and an empirical FDR were found to predict the true FDR within 2–3 fold and are more reliable estimators of confidence than a global Poisson p-value. These methods were then used to reanalyze Johnson et al.'s neuron-restrictive silencer factor (NRSF) ChIP-Seq data without relying on extensive qPCR validated NRSF sites and the presence of NRSF binding motifs for setting thresholds. The methods developed and tested here show considerable promise for reducing false positives and estimating confidence in ChIP-Seq data without any prior knowledge of the chIP target. They are part of a larger open source package freely available from http://useq.sourceforge.net/.
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DOI：
10.1111/1467-9868.00346
发表时间：
2002-01-01
影响因子：
5.8
作者：
Storey, JD
通讯作者：
Storey, JD
影响因子：
7
作者：
Johnson, David S.;Li, Wei;Liu, X. Shirley
通讯作者：
Liu, X. Shirley
影响因子：
48
作者：
Robertson, Gordon;Hirst, Martin;Jones, Steven
通讯作者：
Jones, Steven
影响因子：
7
作者：
Bhinge, Akshay A.;Kim, Jonghwan;Iyer, Vishwanath R.
通讯作者：
Iyer, Vishwanath R.