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CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

Mirjana Efremova, Miquel Vento-Tormo, Sarah A. Teichmann, Roser Vento-Tormo
doi: https://doi.org/10.1101/680926
Mirjana Efremova
1Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
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Miquel Vento-Tormo
2YDEVS software development, Valencia, 46009, Spain
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Sarah A. Teichmann
1Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
3Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0EH, UK
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Roser Vento-Tormo
1Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
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  • For correspondence: rv4@sanger.ac.uk
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Abstract

Cell-cell communication mediated by receptor-ligand complexes is crucial for coordinating diverse biological processes, such as development, differentiation and responses to infection. In order to understand 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 interactions1. Our repository 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, the procedures for inferring cell-cell communication networks from scRNA-seq data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v2.0 is a novel version of our resource that incorporates additional functionalities to allow users to introduce new interacting molecules and reduce the time and resources needed to interrogate large datasets. CellPhoneDB v2.0 is publicly available at https://github.com/Teichlab/cellphonedb and as a user-friendly web interface at http://www.cellphonedb.org/. In our protocol, we demonstrate how to reveal meaningful biological discoveries from CellPhoneDB v2.0 using published data sets.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 24, 2019.
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CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes
Mirjana Efremova, Miquel Vento-Tormo, Sarah A. Teichmann, Roser Vento-Tormo
bioRxiv 680926; doi: https://doi.org/10.1101/680926
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CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes
Mirjana Efremova, Miquel Vento-Tormo, Sarah A. Teichmann, Roser Vento-Tormo
bioRxiv 680926; doi: https://doi.org/10.1101/680926

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