Inference and analysis of cell-cell communication using CellChat.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
17 02 2021
17 02 2021
Historique:
received:
24
04
2020
accepted:
08
01
2021
entrez:
18
2
2021
pubmed:
19
2
2021
medline:
2
3
2021
Statut:
epublish
Résumé
Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer ( http://www.cellchat.org/ ) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.
Identifiants
pubmed: 33597522
doi: 10.1038/s41467-021-21246-9
pii: 10.1038/s41467-021-21246-9
pmc: PMC7889871
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1088Subventions
Organisme : NIAMS NIH HHS
ID : P30 AR075047
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM123731
Pays : United States
Organisme : NIAMS NIH HHS
ID : U01 AR073159
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
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