Ligand-Receptor Interaction Database
Recommended Post: 【Bioinformatics】 Bioinformatics Analysis Index
a. Gene Library
1. Algorithm and Database
① LR interaction score
② scRNA-seq-based
○ CellChat
○ ICELLNET
○ NicheNet
○ SoptSC
○ CytoTalk
○ scTensor
○ CCCExplorer
○ Connectome
③ ST-based
○ spata2
○ CellPhoneDB v3
○ stLearn
○ SCVA
○ MISTy
○ NCEM
○ COMMOT
④ Others
○ squidy
○ IPA (upstream regulator analysis of ingenuity pathway analysis)
2. Ligand-Receptor Library
○ Common target receptors and target ligands
| Organ | Cell type | Receptor | Ligand | Common targeting applications | Ref. |
|---|---|---|---|---|---|
| Liver | Hepatocytes, cancer cells | Asialoglyco-protein | Galactose | Cancer, Wilson’s disease, hemochromatosis | . |
| . | . | . | Galactosamine | . | . |
| . | . | . | Lactose | . | . |
| Liver | Endothelial cells and Kupffer cells | Mannose receptor (C-type lectin receptor) | Mannose | Bacterial infections, inflammation, cardiovascular disease, cancer, cerebral ischemia/stroke, genetic metabolic diseases, Leishmaniasis | . |
| Liver | Hepatocytes | Galactosyl receptor | Galactose | Blood filtration | . |
| Liver | Kupffer cells | Fucose receptor, Lectin B | Fucose | Tissue binding, bio film formation | . |
| Liver, spleen, brain, bone marrow, and lungs | Macrophages | Mannose receptor (C-type lectin receptor) | Mannose | Bacterial infections, inflammation, cardiovascular disease, cancer, cerebral ischemia/stroke, genetic metabolic diseases, Leishmaniasis | . |
| Spleen, lymph nodes, blood, skin | Dendritic cells | Mannose receptor (C-type lectin receptor) | Mannose | Adaptive immune respose/vaccination | . |
| Tumor sites | Malignant cells | Lectin-like receptors (e.g., galectins) | Galactose, lactose, mannose, fucose, Sialic Lewis’ glycosides | Anti-proliferation | . |
| Oral cavity | Buccal cells | Lectin receptors | Lactose and mannose | Bioadhesion | . |
| Eye | Corneal/conjunctival cells | Lectin receptors | Glucose and galactose, chitosan | Conjunctivitis | . |
| Colon | Epithelial cells | Galectin | Galactose | Cancer, bioadhesion | . |
| Lung | Pulmonary cells | Lectin receptors | Galactose | Cystic fibrosis, lung cancer, and pulmonary tuberculosis | . |
| Brain | Neurons | Anionic membranes and lectins | Trimethylated chitosan | Crossing the blood brain barrier, memory impairment | . |
Table. 1. Common target receptors and target ligands
○ ALOX5 ↔︎ ALOX5AP: proinflammatory interaction
○ ANGPTL4 ↔︎ SDC1: adhesive. It may inhibit Wnt signaling
○ BST2 ↔️ LILRA4: anti-inflammatory interaction
○ C3 ↔️ C3AR1: proinflammatory interaction
○ CCL5 ↔️ CCR1: proinflammatory interaction
○ CD28 ↔️ CD80: co-stimulatory
○ CD47 ↔️ SIRPA: innate immunity suppressor
○ COL1A1 ↔︎ SDC1: adhesive
○ CTLA4 ↔️ CD80: co-inhibitory
○ CTLA4 ↔️ CD86: co-inhibitory
○ CX3CL1 ↔️ CX3CR1: anti-inflammatory interaction
○ CXCR3 ↔️ CXCL9: T cell homing interaction
○ CXCR3 ↔️ CXCL10: T cell homing interaction
○ CXCR3 ↔️ CXCL11: T cell homing interaction
○ DNAM1 ↔️ CD155, CD112: cell mediated cytotoxicity
○ DSC2 ↔︎ DSG1: adhesive
○ FGF9 ↔︎ FGFR3: observed in astrocytes
○ FN1 ↔︎ SDC1: adhesive
○ GAS6 ↔︎ TYRO3: innate immunity suppressor
○ HAVCR2 (TIM3) ↔️ LGALS9 (Galectin9): co-inhibitory
○ HLA-F ↔️ LILRB1: anti-inflammatory interaction
○ ICOS ↔️ ICOSLG: co-stimulatory
○ LAIR1 ↔️ LILRB4: suppressive interactions with myeloid cells
○ LAMB3 ↔︎ ITGA6_ITGB1: adhesive
○ LAMB3 ↔︎ ITGA6_ITGB4: adhesive
○ LFA1 ↔️ ICAM1: T cell recruitment
○ MIF ↔︎ CD74_CD44: inflammatory
○ NECTIN1 ↔︎ FGFR3: observed in astrocytes
○ PDCD1 (PD1) ↔️ CD274 (PDL1): co-inhibitory
○ PDCD1 (PD1) ↔️ PDCD1LG2 (PDL2): co-inhibitory
○ POMC ↔️ MC1R: anti-inflammatory interaction
○ PROS1 ↔️ AXL: anti-inflammatory interaction
○ PSAP ↔️ GPR37L1: observed in oligodendrocytes
○ TGFBR3 ↔️ TGFB1: suppressive interactions with myeloid cells
○ TIM-3 (T-cell Ig and mucin domain 3) receptor ↔️ galectin-9 ligand
○ TNFRSF9 ↔️ TNFSF9: co-stimulatory
○ TNFSF10 ↔️ TNFRSF10A: pro-apoptotic interaction
○ VEGF ↔️ NRP1
○ VEGF ↔️ NRP2
Input: 2023.06.12 18:19