CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes
CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes
复制标题
DOI：
10.1038/s41596-020-0292-x
复制
发表时间：
2020-02-26
期刊：
影响因子：
14.8
通讯作者：
Vento-Tormo, Roser
中科院分区：
文献类型：
--
作者：
Efremova, Mirjana;Vento-Tormo, Miquel;Vento-Tormo, Roser
CellPhoneDB结合了一个交互式数据库和一个统计框架，用于探索从单细胞转录组学测量推断的配体-受体相互作用。由配体-受体复合物介导的细胞间通讯对协调多种生物过程至关重要，如发育、分化和炎症。为了研究不同细胞类型的上下文依赖性串扰如何使生理过程进行，我们开发了CellPhoneDB，这是一个新的配体、受体及其相互作用的存储库。与其他库相比，我们的数据库考虑了配体和受体的亚基结构，准确地代表了异质复合物。我们将我们的资源与一个统计框架整合起来，该框架预测了来自单细胞转录组学数据的两种细胞类型之间丰富的细胞相互作用。在这里，我们概述了我们的存储库的结构和内容，提供了从单细胞RNA测序数据推断细胞-细胞通信网络的程序，并提供了一个实用的逐步指南来帮助实现该协议。CellPhoneDB v.2.0是我们的资源的更新版本，它包含了额外的功能，使用户能够引入新的相互作用分子，并减少了查询大型数据集所需的时间和资源。CellPhoneDB v.2.0是公开可用的，包括代码和用户友好的web界面;它可以被没有计算基因组学经验的专家和研究人员使用。在我们的方案中，我们演示了如何使用已发布的数据集评估与CellPhoneDB v.2.0有意义的生物相互作用。对于一个10gb、10000个单元和19个单元类型的数据集，使用5个线程，该协议通常需要大约2小时才能完成，从安装到统计分析和可视化。
CellPhoneDB combines an interactive database and a statistical framework for the exploration of ligand-receptor interactions inferred from single-cell transcriptomics measurements.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 similar to 2 h to complete, from installation to statistical analysis and visualization, for a dataset of similar to 10 GB, 10,000 cells and 19 cell types, and using five threads.