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CellPhoneDB v5:从单细胞多组数据推断细胞与细胞之间的通信

Kevin Troulé¹, Robert Petryszak¹, Batuhan Cakir¹

¹Wellcome Sanger Institute, Cambridge, UK.

Nature protocols

|March 26, 2025

概括

使用单细胞基因组学,CellPhoneDB v5 增强了细胞-细胞通信推断. 这个更新的工具包通过整合各种数据模式来完善对组织生物学和疾病机制的理解.

科学领域:

细胞生物学细胞生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

细胞与细胞之间的沟通对于组织发育,功能和再生至关重要.
单细胞基因组学揭示了体内细胞相互作用和疾病影响.
CellPhoneDB是一个生物信息学工具包,用于从单细胞基因组学数据推断细胞与细胞之间的通信.

研究的目的:

为了介绍CellPhoneDB版本5 (v5) 的协议.
突出新功能,增强细胞-细胞通信推断精度.
为了证明理解组织生物学和疾病的应用.

主要方法:

扩展的联体受体相互作用库,包括非性联体.
为特定的实验设计量身定制的数据库查询.
集成与空间转录组学和单细胞测定转移酶可访问的染色体 (scATAC-seq) 数据的集成,以优先考虑相互作用.
介绍CellPhoneDBViz用于交互式可视化.

主要成果:

CellPhoneDB v5 存储库扩展了三分之一,增加了新的交互功能.
新的策略可以优先考虑特定的细胞相互作用.
提高了推断细胞间通信的精度.
交互式可视化模块有助于结果共享.

结论:

CellPhoneDB v5为细胞间通信推断提供了更高的精度.
新功能为生理微环境中的组织生物学提供了更深入的见解.
该工具包支持研究与破坏细胞所相关的疾病和发育异常.

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