Total Interactions
9,563
Significant ligand-receptor pairs
Analysis Complete
Analysis Results sys04tis01
Published legacy analysis modules for the selected page.
๐ Tissue Level
Cell Communication
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GRN Analysis
โ
Co-expression
โ
Trajectory
โ
DEG Analysis
โ
GO / KEGG
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ToppGene
โ
Motif
โ
Metabolism
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Disease
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Drug Analysis
โ
Full Report
Cell-Cell CommunicationLigand-Receptor Interaction Analysis via CellChat / CellPhoneDB
๐ข
๐ค๏ธ
Signaling Pathways
29
Unique pathways detected
๐ค
Top Sender
Fibroblasts
Most active signaling cell type
๐ฅ
Top Receiver
Neutrophils
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 |
|---|---|---|---|---|---|---|---|
| Endothelial cells | Endothelial cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.292 | 0.0931 |
| Endothelial cells | Macrophages | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.4223 | 0.1346 |
| Endothelial cells | Basal cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.2083 | 0.0664 |
| Endothelial cells | Fibroblasts | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.3306 | 0.1054 |
| Endothelial cells | Alveolar type 2 cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.136 | 0.0434 |
| Endothelial cells | Club cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.1844 | 0.0588 |
| Endothelial cells | T cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.2375 | 0.0757 |
| Endothelial cells | Basophils | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.2532 | 0.0807 |
| Endothelial cells | Alveolar type 1 cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.1462 | 0.0466 |
| Endothelial cells | B cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.2488 | 0.0793 |
| Endothelial cells | Ciliated cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.0646 | 0.0206 |
| Endothelial cells | Mesothelial cells | TGFB1 | TGFBR1 | TGFb | 0.3187 | 0.1302 | 0.0415 |
Showing top 12 rows ยท Download full table above
Gene Regulatory NetworkTranscription Factor Activity & TF-Target Inference (pySCENIC / DoRothEA)
๐๏ธ
TFs Analyzed
95
Transcription factors profiled
๐
TF-Target Pairs
1,988
Significant regulatory relationships
Top Regulatory TFs
CEBPB
235 targets
RUNX1
198 targets
EGR1
173 targets
GATA2
154 targets
FOXA2
143 targets
CEBPA
139 targets
JUN
137 targets
STAT3
133 targets
RB1
122 targets
FOXA1
119 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
Club cells
Most stem-like (highest CytoTRACE score)
๐ฏ
Terminal Cell Type
B cells
Most differentiated (highest pseudotime)
๐ข
Cells Analyzed
50,929
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 | |
|---|---|---|---|
| Homo_sapiens_NA_2025_Rank011_1 | Endothelial cells | 0.2276 | 0.1348 |
| Homo_sapiens_NA_2025_Rank011_3 | Macrophages | 0.7011 | 0.1031 |
| Homo_sapiens_NA_2025_Rank011_4 | Basal cells | 0.3336 | 0.0658 |
| Homo_sapiens_NA_2025_Rank011_6 | Fibroblasts | 0.095 | 0.0614 |
| Homo_sapiens_NA_2025_Rank011_7 | Alveolar type 2 cells | 0.3474 | 0.0764 |
| Homo_sapiens_NA_2025_Rank011_8 | Basal cells | 0.3432 | 0.0684 |
| Homo_sapiens_NA_2025_Rank011_10 | Fibroblasts | 0.2953 | 0.0596 |
| Homo_sapiens_NA_2025_Rank011_11 | Alveolar type 2 cells | 0.4512 | 0.0826 |
| Homo_sapiens_NA_2025_Rank011_12 | Alveolar type 2 cells | 0.4172 | 0.0805 |
| Homo_sapiens_NA_2025_Rank011_13 | Club cells | 0.3811 | 0.07 |
| Homo_sapiens_NA_2025_Rank011_15 | Fibroblasts | 0.2802 | 0.0586 |
| Homo_sapiens_NA_2025_Rank011_16 | Alveolar type 2 cells | 0.4202 | 0.067 |
Showing top 12 rows ยท Download full table above
Differential ExpressionCell Type Marker Genes (Wilcoxon / MAST)
๐
Significant DEGs
1,800
Genes passing adj. p < 0.05 & |log2FC| > 0.5
๐ท๏ธ
Cell Types Compared
18
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 |
|---|---|---|---|---|---|---|---|
| AGER | 72.0301 | 7.8227 | 0 | 0 | 0.9836 | 0.0868 | Alveolar type 1 cells |
| KRT7 | 73.1724 | 7.2778 | 0 | 0 | 0.9968 | 0.2532 | Alveolar type 1 cells |
| CST6 | 61.9191 | 6.5671 | 0 | 0 | 0.8516 | 0.0346 | Alveolar type 1 cells |
| CEACAM6 | 70.0148 | 6.4467 | 0 | 0 | 0.971 | 0.112 | Alveolar type 1 cells |
| SCEL | 67.8563 | 6.4276 | 0 | 0 | 0.9403 | 0.0567 | Alveolar type 1 cells |
| CTSE | 66.2079 | 5.7878 | 0 | 0 | 0.924 | 0.078 | Alveolar type 1 cells |
| FSTL3 | 64.9037 | 5.7728 | 0 | 0 | 0.9018 | 0.0607 | Alveolar type 1 cells |
| TNNC1 | 62.9783 | 5.7495 | 0 | 0 | 0.877 | 0.0626 | Alveolar type 1 cells |
| ARHGEF26 | 63.8739 | 5.538 | 0 | 0 | 0.8997 | 0.0823 | Alveolar type 1 cells |
| SH3RF2 | 55.6074 | 5.5193 | 0 | 0 | 0.7835 | 0.0543 | Alveolar type 1 cells |
| SFTPC | 120.9677 | 6.9205 | 0 | 0 | 0.9988 | 0.9025 | Alveolar type 2 cells |
| ZNF385B | 119.6674 | 6.6695 | 0 | 0 | 0.9683 | 0.1146 | Alveolar type 2 cells |
Showing top 12 rows
Functional EnrichmentGO & KEGG pathway analysis using local hypergeometric ORA
๐งฌ
GO Terms
19,469
Enriched Gene Ontology terms
๐ค๏ธ
KEGG Pathways
3,160
Enriched KEGG pathways
ToppGene AnalysisFunctional enrichment against an internal database background
๐ท๏ธ
Cell Types Analyzed
18
Gene lists submitted
โ
Total Enrichments
30,268
Across all categories
ToppGene Functional Summary
Category distribution and top enriched functional terms.
Motif EnrichmentcisTarget gene-set motif enrichment
๐ฌ
Unique Enriched Motifs
849
Unique motif IDs with NES ≥ 3
โ
Significant Enrichments
3341
Motif-signature-context rows with NES ≥ 3
TF Motif Enrichment Heatmap
Motif enrichment scores across cell types.
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
18
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
20
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
18
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 | Endothelial cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.091 | 33.8162 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Macrophages | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1732 | 74.1375 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Basal cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1029 | 50.1144 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Fibroblasts | Kinase inhibitor | CML / GIST | 5 | 5 | 0.5974 | 93.6806 | 1 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Alveolar type 2 cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.102 | 61.2625 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Club cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1317 | 56.1013 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | T cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.0857 | 28.2163 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Basophils | Kinase inhibitor | CML / GIST | 5 | 5 | 0.6186 | 99.0762 | 1 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Alveolar type 1 cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.0813 | 46.8321 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | B cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.07 | 24.6988 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Ciliated cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1014 | 50.774 | 0 | ABL1,KIT,PDGFRA,PDGFRB,CSF1R |
| Imatinib | Mesothelial cells | Kinase inhibitor | CML / GIST | 5 | 5 | 0.1248 | 53.8462 | 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=SP121&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 |
| GO / KEGG | enrichment_go_barplot.png | Figure (PNG) | ๐ View |
| GO / KEGG | enrichment_kegg_dotplot.png | Figure (PNG) | ๐ View |
| GO / KEGG | enrichment_go.csv | Data (CSV) | ๐ฅ Download |
| GO / KEGG | enrichment_kegg.csv | Data (CSV) | ๐ฅ Download |
| ToppGene | toppgene_summary.png | Figure (PNG) | ๐ View |
| ToppGene | toppgene_results.csv | Data (CSV) | ๐ฅ Download |
| Motif | motif_heatmap.png | Figure (PNG) | ๐ View |
| Motif | motif_enrichment.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 |