Total Interactions
3,073
Significant ligand-receptor pairs
Analysis Complete
Analysis Results sys04tis01
Published legacy analysis modules for the selected page.
๐ Tissue Level
Cell Communication
โ
GRN Analysis
โ
Co-expression
โ
Trajectory
โ
DEG Analysis
โ
GO / KEGG
Not computed
ToppGene
Not computed
Motif
Not computed
Metabolism
โ
Disease
โ
Drug Analysis
โ
Full Report
Cell-Cell CommunicationLigand-Receptor Interaction Analysis via CellChat / CellPhoneDB
๐ข
๐ค๏ธ
Signaling Pathways
27
Unique pathways detected
๐ค
Top Sender
Alveolar type 1 cells
Most active signaling cell type
๐ฅ
Top Receiver
Club cells
Most active receiving cell type
Communication Heatmap
Overall interaction strength between cell types. Rows = sender, columns = receiver.
Communication Network
Network visualization of top 50 cell-cell interactions. Node size = connectivity degree.
Signaling Pathway Activity
Top signaling pathways ranked by total communication score.
๐ Top Ligand-Receptor Interactions
| source | target | ligand | receptor | pathway | ligand_expr | receptor_expr | score |
|---|---|---|---|---|---|---|---|
| Alveolar type 2 cells | Alveolar type 2 cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.2539 | 0.0019 |
| Alveolar type 2 cells | Endothelial cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.1633 | 0.0012 |
| Alveolar type 2 cells | Club cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.3035 | 0.0023 |
| Alveolar type 2 cells | Smooth muscle cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.2073 | 0.0016 |
| Alveolar type 2 cells | B cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.19 | 0.0014 |
| Alveolar type 2 cells | DN T cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.1811 | 0.0014 |
| Alveolar type 2 cells | Fibroblasts | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.144 | 0.0011 |
| Alveolar type 2 cells | Alveolar type 1 cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.1193 | 0.0009 |
| Alveolar type 2 cells | Ciliated cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.2112 | 0.0016 |
| Alveolar type 2 cells | Mesothelial cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.137 | 0.001 |
| Alveolar type 2 cells | Macrophages | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.5749 | 0.0044 |
| Alveolar type 2 cells | CD4+ T cells | TGFB1 | TGFBR1 | TGFb | 0.0076 | 0.237 | 0.0018 |
Showing top 12 rows ยท Download full table above
Gene Regulatory NetworkTranscription Factor Activity & TF-Target Inference (pySCENIC / DoRothEA)
๐๏ธ
TFs Analyzed
90
Transcription factors profiled
๐
TF-Target Pairs
87
Significant regulatory relationships
Top Regulatory TFs
FOXA1
19 targets
RUNX1
18 targets
LEF1
14 targets
RUNX2
10 targets
GATA3
7 targets
GATA2
5 targets
FOS
4 targets
SOX9
3 targets
TCF7
3 targets
EGR1
2 targets
TF Activity Heatmap
Z-score normalized TF expression across cell populations.
Gene Regulatory Network
Red nodes: TFs. Blue: targets. Green edge: activation. Red edge: repression.
Gene Co-expression NetworkWGCNA-style Module Analysis (hdWGCNA)
๐ฆ
Modules Identified
30
Co-expression gene modules
๐งฌ
Genes Analyzed
2,000
Highly variable genes
Module Dendrogram
Hierarchical clustering of co-expression modules based on topological overlap.
Module-Cell Type Association
Module eigengene activity across cell types.
Differentiation TrajectoryCytoTRACE2, Diffusion Pseudotime, PAGA, scVelo / CellRank
๐ฑ
Root Cell Type
Ciliated cells
Most stem-like (highest CytoTRACE score)
๐ฏ
Terminal Cell Type
Alveolar type 1 cells
Most differentiated (highest pseudotime)
๐ข
Cells Analyzed
40,811
Total cells in trajectory
๐
RNA Velocity
Not Available
Requires spliced/unspliced layers
Pseudotime UMAP
CytoTRACE stemness score and diffusion pseudotime projected on UMAP embedding.
PAGA Connectivity Graph
Partition-based graph abstraction showing connectivity between cell type clusters.
Pseudotime Distribution
Pseudotime distribution per cell type, ordered by median pseudotime.
๐ Pseudotime Values
| cell_type | cytotrace_score | dpt_pseudotime | |
|---|---|---|---|
| A01T10R01S01-SKO3_1 | Alveolar type 2 cells | 0.1598 | 0.9269 |
| A01T10R01S01-SKO3_2 | Endothelial cells | 0.1648 | 0.9093 |
| A01T10R01S01-SKO3_3 | Alveolar type 2 cells | 0.1329 | 0.9267 |
| A01T10R01S01-SKO3_4 | Endothelial cells | 0.0832 | 0.9196 |
| A01T10R01S01-SKO3_5 | Club cells | 0.2473 | 0.8998 |
| A01T10R01S01-SKO3_6 | Smooth muscle cells | 0.0769 | 0.9013 |
| A01T10R01S01-SKO3_7 | B cells | 0.0945 | 0.8994 |
| A01T10R01S01-SKO3_8 | Club cells | 0.1345 | 0.9067 |
| A01T10R01S01-SKO3_9 | Endothelial cells | 0.1714 | 0.9055 |
| A01T10R01S01-SKO3_10 | DN T cells | 0.1128 | 0.8941 |
| A01T10R01S01-SKO3_11 | B cells | 0.0941 | 0.8981 |
| A01T10R01S01-SKO3_12 | Club cells | 0.2243 | 0.8725 |
Showing top 12 rows ยท Download full table above
Differential ExpressionCell Type Marker Genes (Wilcoxon / MAST)
๐
Significant DEGs
1,227
Genes passing adj. p < 0.05 & |log2FC| > 0.5
๐ท๏ธ
Cell Types Compared
13
Cell populations analyzed
Volcano Plot
Log2 fold change vs significance. Red: up-regulated. Blue: down-regulated.
Marker Gene Heatmap
Z-score normalized expression of top marker genes per cell type.
๐ Top Marker Genes
| names | scores | logfoldchanges | pvals | pvals_adj | pct_nz_group | pct_nz_reference | cell_type |
|---|---|---|---|---|---|---|---|
| RTKN2 | 62.4757 | 7.488 | 0 | 0 | 0.9375 | 0.1387 | Alveolar type 1 cells |
| COL4A3 | 62.2456 | 6.1236 | 0 | 0 | 0.945 | 0.1606 | Alveolar type 1 cells |
| CAV1 | 39.3276 | 5.2389 | 0 | 0 | 0.6179 | 0.0479 | Alveolar type 1 cells |
| TPRG1 | 24.5292 | 5.1448 | 0 | 0 | 0.3796 | 0.0229 | Alveolar type 1 cells |
| SEMA6D | 41.6281 | 4.8575 | 0 | 0 | 0.6623 | 0.0747 | Alveolar type 1 cells |
| KCND2 | 22.9097 | 4.7889 | 0 | 0 | 0.3602 | 0.0283 | Alveolar type 1 cells |
| AGER | 31.5915 | 4.6604 | 0 | 0 | 0.5009 | 0.0466 | Alveolar type 1 cells |
| COL4A4 | 53.2996 | 4.4187 | 0 | 0 | 0.8787 | 0.2385 | Alveolar type 1 cells |
| CDKL5 | 46.3255 | 4.2573 | 0 | 0 | 0.7717 | 0.1902 | Alveolar type 1 cells |
| NCKAP5 | 59.942 | 4.1681 | 0 | 0 | 0.9775 | 0.5558 | Alveolar type 1 cells |
| SFTPC | 151.6731 | 5.3646 | 0 | 0 | 0.9929 | 0.4477 | Alveolar type 2 cells |
| LGI3 | 52.6223 | 4.4634 | 0 | 0 | 0.3579 | 0.0283 | Alveolar type 2 cells |
Showing top 12 rows
Metabolism AnalysisMetabolic Pathway Activity Scoring (scMetabolism-like approach)
๐งช
Pathways Scored
12
Metabolic pathway gene sets tested
โ
Pathways Detected
12
Pathways with genes expressed in data
๐ท๏ธ
Cell Types Analyzed
13
Cell populations scored
Top Metabolic Pathways
Metabolic Pathway Heatmap
Z-score normalized metabolic pathway activity across cell types.
Top Metabolic Activities
Top pathway-cell type combinations ranked by activity score. Dot size: genes detected.
Disease AssociationDisease Gene Enrichment (scDRS / DisGeNET / OMIM / ToppGene)
๐ฌ
Diseases Tested
15
Disease categories analyzed
โ
Significant Associations
15
Cell type-disease links (adj. p < 0.05)
Top Associated Diseases
Disease Association Heatmap
-Log10(P-value) of disease gene enrichment per cell type.
Top Disease Associations
Dot size: overlap genes. Color: significance.
Drug Target AnalysisDrug-Cell Type Association Scoring (Drug2Cell / DrugBank / DGIdb)
๐
Drugs Screened
18
Drug compounds evaluated
๐ฏ
Drugs with Targets
18
Drugs with target genes detected in data
๐ท๏ธ
Cell Types Analyzed
13
Cell populations scored
Top Associated Drugs
Drug Target Expression Heatmap
Z-score normalized drug target gene expression across cell types.
Top DrugโCell Type Associations
Dot size: % cells expressing targets. Color: number of targets detected.
๐ DrugโCell Type Scores
| drug | cell_type | category | indication | targets_detected | targets_total | mean_target_expr | pct_cells_expressing | deg_overlap | target_genes |
|---|---|---|---|---|---|---|---|---|---|
| Imatinib | Alveolar type 2 cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1665 | 33.2193 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Endothelial cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1319 | 22.4827 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Club cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1505 | 32.9596 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Smooth muscle cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.273 | 46.0967 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | B cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.0493 | 8.9259 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | DN T cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.0746 | 13.3891 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Fibroblasts | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1872 | 32.449 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Alveolar type 1 cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.0643 | 13.9462 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Ciliated cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1445 | 39.2849 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Mesothelial cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1006 | 21.0526 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Macrophages | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1485 | 34.1176 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | CD4+ T cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.2366 | 63.6364 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
Showing top 12 rows ยท Download full table above
Full Analysis ReportComprehensive Summary & Downloads
Interactive HTML Report
Complete analysis report with all figures, key findings, and data summaries in a standalone HTML page.
๐ Open ReportDownload All Results
Download all analysis results including CSV data, PNG figures, and JSON summaries as a compressed archive.
๐ฅ Download ZIPShare Results
Use this permanent link to share these analysis results:
analysis.php?SP_ID=SP239&tisID=sys04tis01
๐ Available Result Files
| Analysis | File | Type | Action |
|---|---|---|---|
| Cell Communication | cellchat_heatmap.png | Figure (PNG) | ๐ View |
| Cell Communication | cellchat_network.png | Figure (PNG) | ๐ View |
| Cell Communication | cellchat_pathway_dotplot.png | Figure (PNG) | ๐ View |
| Cell Communication | cellchat_interactions.csv | Data (CSV) | ๐ฅ Download |
| Cell Communication | cellchat_pathway_summary.csv | Data (CSV) | ๐ฅ Download |
| GRN Analysis | grn_tf_heatmap.png | Figure (PNG) | ๐ View |
| GRN Analysis | grn_network.png | Figure (PNG) | ๐ View |
| GRN Analysis | grn_tf_activity.csv | Data (CSV) | ๐ฅ Download |
| GRN Analysis | grn_tf_targets.csv | Data (CSV) | ๐ฅ Download |
| Co-expression | coexp_dendrogram.png | Figure (PNG) | ๐ View |
| Co-expression | coexp_module_heatmap.png | Figure (PNG) | ๐ View |
| Co-expression | coexp_modules.csv | Data (CSV) | ๐ฅ Download |
| Co-expression | coexp_eigengenes.csv | Data (CSV) | ๐ฅ Download |
| Trajectory | trajectory_pseudotime_umap.png | Figure (PNG) | ๐ View |
| Trajectory | trajectory_paga.png | Figure (PNG) | ๐ View |
| Trajectory | trajectory_pseudotime_boxplot.png | Figure (PNG) | ๐ View |
| Trajectory | trajectory_pseudotime.csv | Data (CSV) | ๐ฅ Download |
| Trajectory | trajectory_paga_connectivity.csv | Data (CSV) | ๐ฅ Download |
| DEG Analysis | deg_volcano.png | Figure (PNG) | ๐ View |
| DEG Analysis | deg_marker_heatmap.png | Figure (PNG) | ๐ View |
| DEG Analysis | deg_top_markers.csv | Data (CSV) | ๐ฅ Download |
| DEG Analysis | deg_significant.csv | Data (CSV) | ๐ฅ Download |
| DEG Analysis | deg_all_results.csv | Data (CSV) | ๐ฅ Download |
| Metabolism | metabolism_heatmap.png | Figure (PNG) | ๐ View |
| Metabolism | metabolism_dotplot.png | Figure (PNG) | ๐ View |
| Metabolism | metabolism_scores.csv | Data (CSV) | ๐ฅ Download |
| Disease | disease_heatmap.png | Figure (PNG) | ๐ View |
| Disease | disease_dotplot.png | Figure (PNG) | ๐ View |
| Disease | disease_enrichment.csv | Data (CSV) | ๐ฅ Download |
| Drug Analysis | drug_heatmap.png | Figure (PNG) | ๐ View |
| Drug Analysis | drug_dotplot.png | Figure (PNG) | ๐ View |
| Drug Analysis | drug_scores.csv | Data (CSV) | ๐ฅ Download |
| Report | sys04tis01_analysis_report.html | Report (HTML) | ๐ Open |
| Report | sys04tis01_summary.json | Summary (JSON) | ๐ฅ Download |