SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures.
SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures.
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SigSeeker：一种用于构建表观遗传特征的峰值调用集成方法。
DOI：
10.1093/bioinformatics/btx276
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Bodine,DavidM
中科院分区：
文献类型：
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作者：
Lichtenberg,Jens;Elnitski,Laura;Bodine,DavidM
动机表观遗传数据是无价的，当确定管理程序的细胞。基于使用下一代测序数据来表征表观遗传标记和转录因子结合，已经开发了许多峰调用方法来确定这些数据中的基因组显著性位点。这样的分析可以产生大量的假阳性预测，这表明由多种算法支持的位点为推断和表征与表观遗传数据相关的调控程序提供了更强的基础。很少有方法集成基于表观遗传的预测的多种方法相结合时，由不同的tools.ResultsThe SigSeeker峰调用合奏使用多种工具来识别峰，并与用户定义的阈值峰重叠和信号强度，它只保留那些峰是一致的跨多个工具。从结果中去除预测为仅通过非常少量的工具共定位的峰、发现仅略微重叠的峰或发现代表近似模型的显著离群值的峰，从而提供简洁且高质量的表观遗传数据集。SigSeeker已经使用转录因子结合和组蛋白修饰ChIP-Seq数据的既定基准进行了验证。这些比较表明，我们的合奏技术的质量超过了单一工具的方法，增强了现有的峰值调用合奏，并导致表观遗传配置文件更高的confidence.Availability和implementationhttp：//sigseeker. org补充信息补充数据可在Bioinformaticsonline。
MotivationEpigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data. Few methodologies integrate epigenetic based predictions of multiple approaches when combining profiles generated by different tools.ResultsThe SigSeeker peak-calling ensemble uses multiple tools to identify peaks, and with user-defined thresholds for peak overlap and signal strength it retains only those peaks that are concordant across multiple tools. Peaks predicted to be co-localized by only a very small number of tools, discovered to be only marginally overlapping, or found to represent significant outliers to the approximation model are removed from the results, providing concise and high quality epigenetic datasets. SigSeeker has been validated using established benchmarks for transcription factor binding and histone modification ChIP-Seq data. These comparisons indicate that the quality of our ensemble technique exceeds that of single tool approaches, enhances existing peak-calling ensembles, and results in epigenetic profiles of higher confidence.Availability and implementationhttp://sigseeker.orgSupplementary informationSupplementary data are available atBioinformaticsonline.