scRNA
Manual Annotation example
Patient data
- Suggested Cell Types
Annotation version 1
Annotation by reference cell type markers
Reference
| Gene | Cell Type |
|---|---|
| CD79A | B cells |
| PTPRC | All leukocytes (B cells, T cells, etc.) |
| CD38 | Activated B cells, plasma cells |
| VPREB3 | B cell development |
| TCL1A | B cells (associated with B cell lymphoma) |
| CD4 | Helper T cells |
| CD8A | Cytotoxic T cells |
| CD8B | Cytotoxic T cells |
| CD3D | All T cells |
| CD3E | All T cells |
| CD3G | All T cells |
| SELL | Naive T cells |
| CD27 | Memory B cells, plasma cells, T cells |
| CCR7 | Naive and central memory T cells |
| CTLA4 | Activated T cells |
| IL2RA | Activated T cells, regulatory T cells |
| GZMB | Cytotoxic T cells, NK cells |
| NKG7 | Cytotoxic T cells, NK cells |
| GZMA | Cytotoxic T cells, NK cells |
| GNLY | NK cells, cytotoxic T cells |
| LYZ | Macrophages, monocytes, other leukocytes |
| MPO | Neutrophils |
| CXCR2 | Neutrophils, some monocytes |
| CD14 | Monocytes, macrophages |
| FCGR3A | NK cells, monocytes, macrophages |
| C1QC | Monocytes, macrophages |
| S100A8 | Inflammatory monocytes, macrophages |
| S100A9 | Inflammatory monocytes, macrophages |
| CD68 | Macrophages, monocytes |
| CD163 | Macrophages, monocytes |
| CD80 | Dendritic cells, B cells |
| CD86 | Dendritic cells, B cells |
| MRC1 | Macrophages, dendritic cells |
| PECAM1 | Endothelial cells, vascular cells |
| CDH5 | Vascular endothelial cells |
| VCAM1 | Vascular endothelial cells |
| VWF | Vascular endothelial cells, platelets |
| ICAM1 | Various cell types (involved in inflammation) |
| ITGAX | Dendritic cells, macrophages |
| CD83 | Mature dendritic cells |
| NRP1 | Dendritic cells, some immune cells |
| CLEC4C | Dendritic cells |
| CD40 | B cells, macrophages, dendritic cells |
| CD44 | Cancer cells |
| EPCAM | Cancer cells |
| KRT18 | Cancer cells |
Resolution 0.2 UMAP
Resolution 0.2 UMAP (label)
Suggested cell types
Cell numbers
Known Marker gene expression (Vertical Dotplot)
Known Marker gene expression (Horizontal Dotplot)
Annotation version 2
Cluster marker and Cell type Table
Cell Types and MK Genes by Cluster
| Cluster | Inferred Cell Type | Key Genes |
|---|---|---|
| 0 | T cells | CD3D, CD2, GIMAP7, CD3G, CD3E, TRAC, BCL11B, … |
| 1 | Macrophages 1 | MS4A7, C5AR1, PLA2G7, SPI1, PILRA, KYNU, DMXL2, … |
| 2 | NK cells | NKG7, GNLY, KLRD1, GZMB, CST7, TYROBP, APOBEC3G, … |
| 3 | B cells | MS4A1, CD79A, BANK1, TNFRSF13C, HLA-DQB1, CD74, … |
| 4 | Regulatory T cells (Tregs) | TIGIT, IL2RA, LINC01943, TNFRSF4, FOXP3, CTLA4, … |
| 5 | Epithelial cells (Cancer) 1 | ELF3, EPCAM, MAL2, PAWR, WFDC2, MYO1B, KRT18, … |
| 6 | Epithelial cells (Cancer) 2 | TM4SF1, KRT18, S100A13, CCND1, IGFBP7, S100A10, … |
| 7 | Dendritic cells | LAMP3, GPR157, IDO1, CSF2RA, RAMP1, CD86, DAP12, … |
| 8 | Mast cells | TPSAB1, TPSB2, GATA2, HPGDS, CPA3, PRG2, KIT, … |
| 9 | Macrophages 2 | MARCO, VSIG4, FABP4, C1QC, PLBD1, TREM1, MSR1, … |
| 10 | Fibroblasts | COL6A2, IGFBP7, FGF2, C11orf96, FERMT2, CALD1, … |
| 11 | Red blood cells | HBA2, HBA1, HBB, SLC25A37 |
| 12 | Alveolar epithelial cells | SFTPB, DDAH1, SFTPD, SFTPA1, SDR16C5, SFTPA2, … |
| 13 | Neutrophils | PI3, FCGR3B, AL021978.1, HCAR3, KCNJ15, S100P, … |
Cell number
Dotplot (Vertical)
Dotplot (Horizontal)
