CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.,Nature Protocols

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CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.
Nature Protocols ( IF 13.1 ) Pub Date : 2020-02-26 , DOI: 10.1038/s41596-020-0292-x
Mirjana Efremova ₁ , Miquel Vento-Tormo ₂ , Sarah A Teichmann _{1,

3} , Roser Vento-Tormo ₁

Affiliation

Cell-cell communication mediated by ligand-receptor complexes is critical to coordinating diverse biological processes, such as development, differentiation and inflammation. To investigate how the context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions. In contrast to other repositories, our database takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, provide procedures for inferring cell-cell communication networks from single-cell RNA sequencing data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v.2.0 is an updated version of our resource that incorporates additional functionalities to enable users to introduce new interacting molecules and reduces the time and resources needed to interrogate large datasets. CellPhoneDB v.2.0 is publicly available, both as code and as a user-friendly web interface; it can be used by both experts and researchers with little experience in computational genomics. In our protocol, we demonstrate how to evaluate meaningful biological interactions with CellPhoneDB v.2.0 using published datasets. This protocol typically takes ~2 h to complete, from installation to statistical analysis and visualization, for a dataset of ~10 GB, 10,000 cells and 19 cell types, and using five threads.

中文翻译：

CellPhoneDB：从多亚基配体-受体复合物的联合表达中推断细胞之间的通讯。

配体-受体复合物介导的细胞间通讯对于协调多种生物学过程（例如发育，分化和炎症）至关重要。为了研究不同细胞类型的背景相关串扰如何使生理过程得以进行，我们开发了CellPhoneDB，这是一种新型的配体，受体及其相互作用的储存库。与其他存储库相反，我们的数据库考虑了配体和受体的亚基结构，可准确代表异聚复合物。我们将资源与统计框架集成在一起，该框架从单细胞转录组学数据预测两种细胞类型之间的丰富细胞相互作用。在这里，我们概述了存储库的结构和内容，提供从单细胞RNA测序数据推断细胞间通信网络的程序，并提供实用的分步指南以帮助实现该协议。CellPhoneDB v.2.0是我们资源的更新版本，其中合并了其他功能，以使用户能够引入新的相互作用分子并减少询问大型数据集所需的时间和资源。CellPhoneDB v.2.0可以作为代码和用户友好的Web界面公开获得；很少有计算基因组学经验的专家和研究人员都可以使用它。在我们的协议中，我们演示了如何使用已发布的数据集评估与CellPhoneDB v.2.0有意义的生物学相互作用。从安装到统计分析和可视化，该协议通常需要2个小时才能完成，

更新日期：2020-02-26

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