Eukaryotic gene transcription is regulated by a large cohort of chromatin-associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 uses a hierarchical strategy for normalization of ChIP-seq data and assesses within-group variability of ChIP-seq signals based on an empirical Bayes framework. In this framework, MAnorm2 allows for abundant differential ChIP-seq signals between groups of samples as well as very different global within-group variability between groups. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, especially when the groups of samples being compared had distinct global within-group variability.

中文翻译：

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MAnorm2 用于定量比较 ChIP-seq 样本组

真核基因转录受一大群染色质相关蛋白的调控，推断它们在细胞环境之间的差异结合位点需要对相应的 ChIP-seq 数据进行严格的比较。我们提出了 MAnorm2，这是一种用于定量比较 ChIP-seq 样本组的新计算工具。MAnorm2 使用分层策略对 ChIP-seq 数据进行标准化，并基于经验贝叶斯框架评估 ChIP-seq 信号的组内变异性。在这个框架中，MAnorm2 允许样本组之间存在丰富的差异 ChIP-seq 信号以及组间非常不同的全局组内变异性。使用许多真实的 ChIP-seq 数据集，我们观察到 MAnorm2 明显优于现有的差分 ChIP-seq 分析工具，