Compendium of available lists of ligand-receptor pairs in literature

This compendium has been created to collect lists of ligand-receptor pairs and interactions for surface-secreted proteins that are available in literature.

How to cite

If you use any of the lists collected in this repository, please cite the respective article.

Also, cite the article where this repository was published:

• Armingol, E., Officer, A., Harismendy, O. & Lewis, N.E. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet (2020) https://doi.org/10.1038/s41576-020-00292-x

Information about collected lists

Article	Organism	Number of LR pairs	Downstream genes?	Protein Complexes?	Functional Annotations?	Associated Tool
Kirouac et al. (2010)	Human	232
Qiao et al. (2014)	Human	933
Ramilowski et al. (2015)	Human	2,422
Choi et al. (2015)	Human	1,427
Pavlicev et al. (2017)	Human	1,006
Vento-Tormo et al. (2018) & Efremova et al. (2020)	Human	878		X		CellPhoneDB
Wang et al. (2019)	Human	2,649			X	iTalk
Ximerakis et al. (2019) & BaderLab (baderlab.org/CellCellInteractions)	Human	115,900
Browaeys et al. (2019)	Human	12,659	X			NicheNet
Noël et al. (2020)	Human	380		X	X	ICELLNET
Cabello-Aguilar et al. (2020)	Human	3,251				SingleCellSignalR
Jin et al. (2020)	Human	2,005		X	X	CellChat
Hou et al. (2020)	Human	2,187				NATMI
Shao et al. (2020)	Human	3,398
Ding et al. (2016)	Mouse	561
Yuzwa et al. (2016)	Mouse	949
Skelly et al. (2018)	Mouse	2,009
Sheikh et al. (2019)	Mouse	1,710
Baccin et al. (2020)	Mouse	721		X	X	RNA-Magnet (Algorithm)
Cain et al. (2020)	Mouse	2,356
Jin et al. (2020)	Mouse	2,021		X	X	CellChat
Shao et al. (2020)	Mouse	2,033
Raredon et al. (2019)	Mammals	269			X
Armingol et al. (2020)	C. elegans	245			X	cell2cell

References for Human Lists

• Kirouac et al. (2010) Dynamic interaction networks in a hierarchically organized tissue | Article | LR pairs
• Qiao et al. (2014) Intercellular network structure and regulatory motifs in the human hematopoietic system | Article | LR pairs
• Ramilowski et al. (2015) A draft network of ligand–receptor-mediated multicellular signalling in human | Article | LR pairs
• Choi et al. (2015) Transcriptome Analysis of Individual Stromal Cell Populations Identifies Stroma-Tumor Crosstalk in Mouse Lung Cancer Model | Article | LR pairs
• Pavlicev et al. (2017) Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface | Article | LR pairs
• Vento-Tormo et al. (2018) Single-cell reconstruction of the early maternal-fetal interface in humans // Efremova et al. (2020) CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes | Article 1 | Article 2 | LR pairs
• Wang et al. (2019) iTALK: an R Package to Characterize and Illustrate Intercellular Communication | Article | LR pairs
• Ximerakis et al. (2019) Single-cell transcriptomic profiling of the aging mouse brain | Article | LR pairs
• Browaeys et al. (2019) NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes | Article | LR pairs
• Noël et al. (2020) ICELLNET: a transcriptome-based framework to dissect intercellular communication | Article | LR pairs
• Cabello-Aguilar et al. (2020) SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics | Article | LR pairs
• Jin et al. (2020) Inference and analysis of cell-cell communication using CellChat | Article | LR pairs
• Hou et al. (2020) Predicting cell-to-cell communication networks using NATMI | Article | LR pairs
• Shao et al. (2020) CellTalkDB: a manually curated database of ligand–receptor interactions in humans and mice | Article | LR pairs

References for Mouse Lists

• Ding et al. (2016) A cell-type-resolved liver proteome | Article | LR pairs
• Yuzwa et al. (2016) Proneurogenic ligands defined by modeling developing cortex growth factor communication networks | Article | LR pairs
• Skelly et al. (2018) Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart | Article | LR pairs
• Sheikh et al. (2019) Systematic identification of cell-cell communication networks in the developing brain | Article | LR pairs
• Baccin et al. (2020) Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization | Article | LR pairs
• Cain et al. (2020) Quantitative single-cell interactomes in normal and virus-infected mouse lungs | Article | LR pairs
• Jin et al. (2020) Inference and analysis of cell-cell communication using CellChat | Article | LR pairs
• Shao et al. (2020) CellTalkDB: a manually curated database of ligand–receptor interactions in humans and mice | Article | LR pairs

References for Lists of Other Organisms

• [Mammals]: Raredon et al. (2019) Single-cell connectomic analysis of adult mammalian lungs | Article | LR pairs
• [C. elegans]: Armingol et al. (2020) Inferring the spatial code of cell-cell interactions and communication across a whole animal body | Article | LR pairs