COMMOTR includes curated ligand-receptor databases from CellChat
and CellPhoneDB. These databases are stored as RDS files and loaded via
ligand_receptor_database.
Details
Available databases:
CellChat (Mouse): 2,019 ligand-receptor interactions
CellChat (Human): 1,939 ligand-receptor interactions
CellChat (Zebrafish): 2,774 ligand-receptor interactions
CellPhoneDB v4.0 (Mouse): 1,410 ligand-receptor interactions
CellPhoneDB v4.0 (Human): 1,680 ligand-receptor interactions
Each database contains:
- ligand
Ligand gene name(s), underscore-separated for complexes
- receptor
Receptor gene name(s), underscore-separated for complexes
- pathway
Signaling pathway name
- signaling_type
Type: Secreted Signaling, Cell-Cell Contact, or ECM-Receptor
References
CellChat: Jin, S. et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun 12, 1088 (2021).
CellPhoneDB: Efremova, M. et al. CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat Protoc 15, 1484-1506 (2020).