We developed Lisa ( http://lisa.cistrome.org/ ) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.

中文翻译：

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Lisa：通过公共染色质可及性和 ChIP-seq 数据的综合建模推断转录调节因子

我们开发了 Lisa ( http://lisa.cistrome.org/ ) 来预测差异表达或共表达基因组的转录调节因子 (TR)。基于输入的基因集，Lisa 首先使用组蛋白标记 ChIP-seq 和染色质可及性概况来构建与这些基因调控相关的染色质模型。使用 TR ChIP-seq 峰或估算的 TR 结合位点，Lisa 使用计算机删除来探测染色质模型以找到最相关的 TR。应用于源自靶向 TF 扰动实验的基因集，Lisa 提高了推算 TR cistromes 的性能，并且在识别扰动 TR 方面优于其他方法。