title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated
Spatial Omics Analysis - Reference Data
Reference tables for cell type markers, immune checkpoints, ligand-receptor pairs, and validation methods.
Cell Type Marker Genes
Use these to assign cell types when user does not provide annotations.
| Cell Type |
Key Markers |
Extended Markers |
| Epithelial |
CDH1, EPCAM, KRT18, KRT19 |
KRT8, KRT14, MUC1 |
| Mesenchymal/Fibroblast |
VIM, COL1A1, COL3A1, FAP, ACTA2 |
PDGFRA, PDGFRB |
| Endothelial |
PECAM1, VWF, CDH5 |
KDR, FLT1 |
| T cell (CD8+) |
CD8A, CD8B |
GZMA, GZMB, PRF1, IFNG |
| T cell (CD4+) |
CD4 |
IL2, IL4, IL17A, FOXP3 (Treg) |
| Regulatory T cell |
FOXP3, IL2RA |
CTLA4, TIGIT |
| B cell |
CD19, MS4A1, CD79A |
IGHG1, IGHM |
| Plasma cell |
SDC1 (CD138), XBP1 |
IGHG1, MZB1 |
| M1 Macrophage |
CD68, NOS2, TNF |
IL1B, CXCL10 |
| M2 Macrophage |
CD68, CD163, MRC1 |
ARG1, IL10 |
| Dendritic cell |
ITGAX (CD11c), HLA-DRA |
CD80, CD86 |
| NK cell |
NCAM1 (CD56), NKG7 |
GNLY, KLRD1 |
| Neutrophil |
FCGR3B, CXCR2 |
S100A8, S100A9 |
| Mast cell |
KIT, TPSAB1 |
CPA3, HDC |
| Neuronal |
SNAP25, SYP, MAP2, NEFL |
RBFOX3, TUBB3 |
| Hepatocyte |
ALB, HNF4A, CYP3A4 |
APOB, TTR |
Cell Type Assignment Rules
- Check each gene against known cell type markers
- Use HPA tissue/cell type expression data for validation
- Confidence: high (3+ markers match), medium (2 markers), low (1 marker)
Immune Checkpoint Reference
| Checkpoint |
Gene |
Ligand |
Therapeutic Antibody |
| PD-1/PD-L1 |
PDCD1/CD274 |
CD274, PDCD1LG2 |
Pembrolizumab, Nivolumab, Atezolizumab |
| CTLA-4 |
CTLA4 |
CD80, CD86 |
Ipilimumab |
| TIM-3 |
HAVCR2 |
LGALS9 |
Sabatolimab |
| LAG-3 |
LAG3 |
HLA class II |
Relatlimab |
| TIGIT |
TIGIT |
PVR, PVRL2 |
Tiragolumab |
| VISTA |
VSIR |
PSGL1 |
- |
Ligand-Receptor Pairs
Known ligand-receptor pairs to check in SVG lists:
| Category |
Ligand |
Receptor |
| Growth factors |
EGF |
EGFR |
| Growth factors |
HGF |
MET |
| Growth factors |
VEGF |
KDR |
| Growth factors |
FGF |
FGFR |
| Growth factors |
PDGF |
PDGFRA/B |
| Cytokines |
TNF |
TNFR |
| Cytokines |
IL6 |
IL6R |
| Cytokines |
IFNG |
IFNGR |
| Cytokines |
TGFB1 |
TGFBR1/2 |
| Chemokines |
CXCL12 |
CXCR4 |
| Chemokines |
CCL2 |
CCR2 |
| Chemokines |
CXCL10 |
CXCR3 |
| Immune checkpoints |
CD274 (PD-L1) |
PDCD1 (PD-1) |
| Immune checkpoints |
CD80/CD86 |
CTLA4 |
| Immune checkpoints |
LGALS9 |
HAVCR2 (TIM-3) |
| Notch signaling |
DLL1/3/4 |
NOTCH1/2/3/4 |
| Notch signaling |
JAG1/2 |
NOTCH1/2 |
| Wnt signaling |
WNT ligands |
FZD receptors |
| Adhesion |
CDH1 |
CDH1 (homotypic) |
| Adhesion |
ITGA/B integrins |
ECM |
| Hedgehog |
SHH |
PTCH1 |
Enrichment Interpretation Guide
| Pathway Category |
Spatial Interpretation |
| Signaling (RTK, Wnt, Notch, Hedgehog) |
Cell-cell communication |
| Metabolic pathways |
Tissue metabolic zonation |
| Immune pathways |
Immune infiltration/exclusion |
| ECM/adhesion |
Tissue structure and remodeling |
| Cell cycle/proliferation |
Growth zones |
| Apoptosis/stress |
Damage zones |
Validation Recommendations Template
| Priority |
Target |
Method |
Rationale |
Feasibility |
| High |
Key SVG |
smFISH / RNAscope |
Validate spatial pattern at single-molecule level |
Medium |
| High |
Druggable target |
IHC on serial sections |
Confirm protein expression in spatial domain |
High |
| High |
Ligand-receptor pair |
Proximity ligation assay (PLA) |
Confirm physical interaction at tissue level |
Medium |
| Medium |
Domain markers |
Multiplexed IF (CODEX/IBEX) |
Validate multiple markers simultaneously |
Low-Medium |
| Medium |
Pathway |
Spatial metabolomics (MALDI/DESI) |
Confirm metabolic pathway activity |
Low |
| Low |
Novel interaction |
Co-culture + conditioned media |
Functional validation of predicted interaction |
Medium |
Literature Search Strategy
- Tissue + spatial:
"{tissue} spatial transcriptomics"
- Disease + spatial:
"{disease} spatial omics"
- Gene + tissue:
"{top_gene} {tissue} expression" for key SVGs
- Zonation (if relevant):
"{tissue} zonation gene expression"
- Technology:
"{technology} {tissue}"
