⚙ How is this computed? Methods: Data Formats
Analysis Complete

Analysis Results sys05tis01

Published legacy analysis modules for the selected page.

Species: SP239
Tissue: sys05tis01
Generated: 2026-08-07 23:48
Modules: 5
📊 Tissue Level
📡
376
Cell Interactions
🧬
32
TF-Target Pairs
📊
497
Significant DEGs
🎯
45
GO Terms
🛤️
40
KEGG Pathways
🔗
30
Co-exp Modules
⚗️
—
Metab. Pathways
🏥
4
Disease Links
💊
—
Drugs Matched
📡 Cell Communication ✓ 🧬 GRN Analysis ✓ 🔗 Co-expression ✓ 🔀 Trajectory Not computed 📊 DEG Analysis ✓ 🎯 GO / KEGG Not computed 🧪 ToppGene Not computed 🔠 Motif Not computed ⚗️ Metabolism Not computed 🏥 Disease ✓ 💊 Drug Analysis Not computed 📄 Full Report
📡

Cell-Cell CommunicationLigand-Receptor Interaction Analysis via CellChat / CellPhoneDB

🔢
Total Interactions
376
Significant ligand-receptor pairs
🛤️
Signaling Pathways
23
Unique pathways detected
📤
Top Sender
Stellate cells
Most active signaling cell type
📥
Top Receiver
Endothelial cells
Most active receiving cell type
Communication Heatmap

Communication Heatmap

Overall interaction strength between cell types. Rows = sender, columns = receiver.

🔍 Full Size
Communication Network

Communication Network

Network visualization of top 50 cell-cell interactions. Node size = connectivity degree.

🔍 Full Size
Signaling Pathway Activity

Signaling Pathway Activity

Top signaling pathways ranked by total communication score.

🔍 Full Size

📋 Top Ligand-Receptor Interactions

📥 All Interactions 📥 Pathway Summary
source target ligand receptor pathway ligand_expr receptor_expr score
Kupffer cells Kupffer cells TGFB1 TGFBR1 TGFb 0.0381 0.1471 0.0056
Kupffer cells Endothelial cells TGFB1 TGFBR1 TGFb 0.0381 0.1065 0.0041
Kupffer cells Hepatocytes TGFB1 TGFBR1 TGFb 0.0381 0.1283 0.0049
Kupffer cells Stellate cells TGFB1 TGFBR1 TGFb 0.0381 0.1395 0.0053
Kupffer cells DN T cells TGFB1 TGFBR1 TGFb 0.0381 0.1484 0.0056
Endothelial cells Kupffer cells TGFB1 TGFBR1 TGFb 0.0191 0.1471 0.0028
Endothelial cells Endothelial cells TGFB1 TGFBR1 TGFb 0.0191 0.1065 0.002
Endothelial cells Hepatocytes TGFB1 TGFBR1 TGFb 0.0191 0.1283 0.0025
Endothelial cells Stellate cells TGFB1 TGFBR1 TGFb 0.0191 0.1395 0.0027
Endothelial cells DN T cells TGFB1 TGFBR1 TGFb 0.0191 0.1484 0.0028
Hepatocytes Kupffer cells TGFB1 TGFBR1 TGFb 0.0026 0.1471 0.0004
Hepatocytes Endothelial cells TGFB1 TGFBR1 TGFb 0.0026 0.1065 0.0003
Showing top 12 rows · Download full table above
🧬

Gene Regulatory NetworkTranscription Factor Activity & TF-Target Inference (pySCENIC / DoRothEA)

🎛️
TFs Analyzed
90
Transcription factors profiled
🔗
TF-Target Pairs
32
Significant regulatory relationships

Top Regulatory TFs

HNF4A 15 targets
LEF1 5 targets
GATA3 4 targets
RUNX2 3 targets
TCF7 2 targets
SOX9 1 targets
IRF4 1 targets
BATF 1 targets
TF Activity Heatmap

TF Activity Heatmap

Z-score normalized TF expression across cell populations.

🔍 Full Size 📥 TF Activity 📥 TF-Target Pairs
Gene Regulatory Network

Gene Regulatory Network

Red nodes: TFs. Blue: targets. Green edge: activation. Red edge: repression.

🔍 Full Size 📥 TF Activity 📥 TF-Target Pairs
🔗

Gene Co-expression NetworkWGCNA-style Module Analysis (hdWGCNA)

📦
Modules Identified
30
Co-expression gene modules
🧬
Genes Analyzed
2,000
Highly variable genes
Module Dendrogram

Module Dendrogram

Hierarchical clustering of co-expression modules based on topological overlap.

🔍 Full Size 📥 Gene Modules 📥 Eigengenes
Module-Cell Type Association

Module-Cell Type Association

Module eigengene activity across cell types.

🔍 Full Size 📥 Gene Modules 📥 Eigengenes
📊

Differential ExpressionCell Type Marker Genes (Wilcoxon / MAST)

📈
Significant DEGs
497
Genes passing adj. p < 0.05 & |log2FC| > 0.5
🏷️
Cell Types Compared
5
Cell populations analyzed
Volcano Plot

Volcano Plot

Log2 fold change vs significance. Red: up-regulated. Blue: down-regulated.

Marker Gene Heatmap

Marker Gene Heatmap

Z-score normalized expression of top marker genes per cell type.

📋 Top Marker Genes

📥 Top Markers 📥 All Significant DEGs 📥 Full DEG Results
names scores logfoldchanges pvals pvals_adj pct_nz_group pct_nz_reference cell_type
IL7R 7.6776 7.6478 0 0 0.3263 0.0034 DN T cells
ITK 5.0746 7.4406 0 0 0.2158 0.0022 DN T cells
SKAP1 11.9498 7.2023 0 0 0.5105 0.0112 DN T cells
SCML4 7.4068 7.1725 0 0 0.3158 0.0048 DN T cells
SLAMF6 6.0383 6.8682 0 0 0.2579 0.0041 DN T cells
PTPRC 14.3377 6.4066 0 0 0.6211 0.0312 DN T cells
RIPOR2 7.2217 6.3575 0 0 0.3105 0.0077 DN T cells
CAMK4 3.4356 6.3333 0.0006 0.018 0.1474 0.0029 DN T cells
ST8SIA4 5.2715 6.2922 0 0 0.2263 0.0048 DN T cells
STK17B 3.6769 6.1763 0.0002 0.0081 0.1579 0.0032 DN T cells
STAB2 36.2312 6.87 0 0 0.8697 0.082 Endothelial cells
PTPRB 25.3227 5.9555 0 0 0.6138 0.0377 Endothelial cells
Showing top 12 rows
🏥

Disease AssociationDisease Gene Enrichment (scDRS / DisGeNET / OMIM / ToppGene)

🔬
Diseases Tested
15
Disease categories analyzed
✅
Significant Associations
4
Cell type-disease links (adj. p < 0.05)

Top Associated Diseases

Multiple sclerosis Inflammatory bowel disease Type 2 diabetes Cardiovascular disease
Disease Association Heatmap

Disease Association Heatmap

-Log10(P-value) of disease gene enrichment per cell type.

Top Disease Associations

Top Disease Associations

Dot size: overlap genes. Color: significance.

📥 Disease Enrichment Data
📄

Full Analysis ReportComprehensive Summary & Downloads

📊

Interactive HTML Report

Complete analysis report with all figures, key findings, and data summaries in a standalone HTML page.

📄 Open Report
📦

Download All Results

Download all analysis results including CSV data, PNG figures, and JSON summaries as a compressed archive.

📥 Download ZIP
🔗

Share Results

Use this permanent link to share these analysis results:

analysis.php?SP_ID=SP239&tisID=sys05tis01

📁 Available Result Files

Analysis File Type Action
Cell Communication cellchat_heatmap.png Figure (PNG) 🔍 View
Cell Communication cellchat_network.png Figure (PNG) 🔍 View
Cell Communication cellchat_pathway_dotplot.png Figure (PNG) 🔍 View
Cell Communication cellchat_interactions.csv Data (CSV) 📥 Download
Cell Communication cellchat_pathway_summary.csv Data (CSV) 📥 Download
GRN Analysis grn_tf_heatmap.png Figure (PNG) 🔍 View
GRN Analysis grn_network.png Figure (PNG) 🔍 View
GRN Analysis grn_tf_activity.csv Data (CSV) 📥 Download
GRN Analysis grn_tf_targets.csv Data (CSV) 📥 Download
Co-expression coexp_dendrogram.png Figure (PNG) 🔍 View
Co-expression coexp_module_heatmap.png Figure (PNG) 🔍 View
Co-expression coexp_modules.csv Data (CSV) 📥 Download
Co-expression coexp_eigengenes.csv Data (CSV) 📥 Download
DEG Analysis deg_volcano.png Figure (PNG) 🔍 View
DEG Analysis deg_marker_heatmap.png Figure (PNG) 🔍 View
DEG Analysis deg_top_markers.csv Data (CSV) 📥 Download
DEG Analysis deg_significant.csv Data (CSV) 📥 Download
DEG Analysis deg_all_results.csv Data (CSV) 📥 Download
Disease disease_heatmap.png Figure (PNG) 🔍 View
Disease disease_dotplot.png Figure (PNG) 🔍 View
Disease disease_enrichment.csv Data (CSV) 📥 Download
Report sys05tis01_analysis_report.html Report (HTML) 📄 Open
Report sys05tis01_summary.json Summary (JSON) 📥 Download