因果CCC:一个探索细胞内因果通路的网络服务器,使细胞-细胞通信成为可能
Louise Dupuis1, Orianne Debeaupuis1,2, Franck Simon1
1CNRS UMR168, Institut Curie, 75005 Paris, France.
Nucleic acids research
|May 14, 2025
概括
因果CCC从单细胞数据中重建基因-基因相互作用路径,整合上游和下游信号,以全面了解细胞-细胞通信,而不仅仅是连接体-受体得分.
科学领域:
- 计算生物学 计算生物学
- 系统生物学 系统生物学
- 基因组学就是基因组学.
背景情况:
- 细胞-细胞通信 (CCC) 对生物过程至关重要.
- 目前的CCC方法主要集中在联体受体相互作用上,在理解细胞内途径集成方面存在差距.
研究的目的:
- 介绍CausalCCC,一个交互式Web服务器,用于重建CCC中的基因-基因相互作用途径.
- 通过整合上游和下游信号,使细胞交叉通话的全面分析成为可能.
主要方法:
- 因果CCC集成了基于多变量信息的诱导因果关系,用于因果网络的重建.
- 它包含内部计算的联体受体对 (LIANA+) 或用户定义的对.
- 网络服务器提供交互式可视化工具和教程.
主要成果:
- 因果CCC成功地从单细胞和空间转录基因数据中重建了扩展的CCC路径.
- 在NicheNet,CellChat和Misty的数据集上展示了应用.
- 提供独特的交互可视化,用于探索多细胞类型交叉通话.
结论:
- 因果CCC解决了除了简单的连接体-受体评分之外的综合CCC通路分析的需求.
- 它使研究人员能够在单细胞和空间转录学中探索复杂的细胞交叉通话.
- 通过详细的CCC路径重建,为推进生物过程理解提供了有价值的工具.
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