Compendium of available lists of ligand-receptor pairs in literature
January 20, 2023 · View on GitHub
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 22, 71–88 (2021). 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? | Metabolites? | 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 | |||||
| Turei et al. (2021) | Human | 74,909 | X | X | X | ||
| Zheng et al. (2022) | Human | 440 | X | MEBOCOST | |||
| Dimitrov et al. (2022) | Human | 4,701 | X | LIANA | |||
| Zhao et al. (2023) | Human | 190 | X | NeuronChat | |||
| 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 | |||||
| Dimitrov et al. (2022) | Mouse | 3,998 | X | LIANA | |||
| Zhao et al. (2023) | Mouse | 183 | X | NeuronChat | |||
| Raredon et al. (2019) | Mammals | 269 | X | ||||
| Armingol et al. (2022) | C. elegans | 245 | X | cell2cell | |||
| Liu et al. (2022) | Drosophila | 197 | X | FlyPhoneDB | |||
| Xu et al. (2022) | Plants | 1,751 - 3,762 | PlantPhoneDB |
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
- Turei et al. (2021) Integrated intra- and intercellular signaling knowledge for multicellular omics analysis | Article | LR pairs
- Zheng et al. (2022) MEBOCOST: Metabolic Cell-Cell Communication Modeling by Single Cell Transcriptome | Article | LR pairs
- Dimitrov et al. (2022) Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data | Article | LR pairs
- Zhao et al. (2023) Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat | 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
- Dimitrov et al. (2022) Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data | Article | LR pairs
- Zhao et al. (2023) Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat | 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. (2022) Inferring a spatial code of cell-cell interactions across a whole animal body | Article | LR pairs
- [Drosophila]: Liu et al. (2022) FlyPhoneDB: an integrated web-based resource for cell–cell communication prediction in Drosophila | Article | LR pairs
- [Plants]: Xu et al. (2022) PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication | Article | LR pairs