SCENIC+:增强剂和基因调控网络的单细胞多原子推断
Carmen Bravo González-Blas1,2, Seppe De Winter1,2, Gert Hulselmans1,2
1VIB Center for Brain & Disease Research, Leuven, Belgium.
Nature methods
|July 13, 2023
概括
SCENIC+通过将增强剂连接到向基因和转录因子来推断基因调节网络. 这种方法增强了对各种物种和细胞类型的基因调节的理解.
科学领域:
- 基因组学就是基因组学.
- 系统生物学 系统生物学
- 计算生物学 计算生物学
背景情况:
- 在单细胞中对染色质可访问性和基因表达的联合分析为增强器驱动的基因调控网络 (GRNs) 提供了洞察力.
- 现有的方法在准确识别转录因子 (TF) 和它们的监管目标方面可能面临局限性.
研究的目的:
- 介绍SCENIC+,一种新的计算方法,用于从单细胞多omics数据中推断增强器驱动的GRNs.
- 提高TF的准确性和全面性,并增强器件识别.
主要方法:
- SCENIC+预测基因组增强剂,识别候选上游TFs,并将它们与目标基因联系起来.
- 一个精心策划和聚类的图案收集超过3万个图案被用来提高TF识别精度和回忆.
- 该方法是基于人类,小鼠和Drosophila的各种数据集进行基准测试的.
主要成果:
- 在多种物种和细胞类型中,SCENIC+成功预测了增强剂,TF和基因.
- 与现有方法相比,该方法在TF识别方面表现更好.
- 应用包括研究人类和小鼠之间的保存GRNs,分析差异化轨迹,并评估TF扰动效应.
结论:
- 在单细胞分辨率下,SCENIC+提供了一个强大的框架来破译增强器驱动的GRNs.
- 该方法有助于比较基因组学和研究基因调节动态.
- SCENIC+是一个有价值的工具,有助于我们更好地理解基因调节机制在发育和疾病中的作用.
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