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

Analysis Results sys04

Published legacy analysis modules for the selected page.

Species: SP239
System: sys04
Generated: 2026-08-07 23:48
Modules: 5
๐Ÿ“Š System Level
๐Ÿ“ก
3,073
Cell Interactions
๐Ÿงฌ
87
TF-Target Pairs
๐Ÿ“Š
1,227
Significant DEGs
๐ŸŽฏ
117
GO Terms
๐Ÿ›ค๏ธ
104
KEGG Pathways
๐Ÿ”—
30
Co-exp Modules
โš—๏ธ
โ€”
Metab. Pathways
๐Ÿฅ
15
Disease Links
๐Ÿ’Š
โ€”
Drugs Matched
๐Ÿ“ก Cell Communication โœ“ ๐Ÿงฌ GRN Analysis โœ“ ๐Ÿ”— Co-expression โœ“ ๐Ÿ”€ Trajectory Not computed ๐Ÿ“Š DEG Analysis โœ“ ๐ŸŽฏ GO / KEGG Not computed ๐Ÿงช ToppGene Not computed ๐Ÿ”  Motif Not computed โš—๏ธ Metabolism Not computed ๐Ÿฅ Disease โœ“ ๐Ÿ’Š Drug Analysis Not computed ๐Ÿ“„ Full Report
๐Ÿ“ก

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

๐Ÿ”ข
Total Interactions
3,073
Significant ligand-receptor pairs
๐Ÿ›ค๏ธ
Signaling Pathways
27
Unique pathways detected
๐Ÿ“ค
Top Sender
Alveolar type 1 cells
Most active signaling cell type
๐Ÿ“ฅ
Top Receiver
Club cells
Most active receiving cell type
Communication Heatmap

Communication Heatmap

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

๐Ÿ” Full Size
Communication Network

Communication Network

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

๐Ÿ” Full Size
Signaling Pathway Activity

Signaling Pathway Activity

Top signaling pathways ranked by total communication score.

๐Ÿ” Full Size

๐Ÿ“‹ Top Ligand-Receptor Interactions

๐Ÿ“ฅ All Interactions ๐Ÿ“ฅ Pathway Summary
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
๐Ÿงฌ

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

๐ŸŽ›๏ธ
TFs Analyzed
90
Transcription factors profiled
๐Ÿ”—
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

TF Activity Heatmap

Z-score normalized TF expression across cell populations.

๐Ÿ” Full Size ๐Ÿ“ฅ TF Activity ๐Ÿ“ฅ TF-Target Pairs
Gene Regulatory Network

Gene Regulatory Network

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

๐Ÿ” Full Size ๐Ÿ“ฅ TF Activity ๐Ÿ“ฅ TF-Target Pairs
๐Ÿ”—

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

๐Ÿ“ฆ
Modules Identified
30
Co-expression gene modules
๐Ÿงฌ
Genes Analyzed
2,000
Highly variable genes
Module Dendrogram

Module Dendrogram

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

๐Ÿ” Full Size ๐Ÿ“ฅ Gene Modules ๐Ÿ“ฅ Eigengenes
Module-Cell Type Association

Module-Cell Type Association

Module eigengene activity across cell types.

๐Ÿ” Full Size ๐Ÿ“ฅ Gene Modules ๐Ÿ“ฅ Eigengenes
๐Ÿ“Š

Differential ExpressionCell Type Marker Genes (Wilcoxon / MAST)

๐Ÿ“ˆ
Significant DEGs
1,227
Genes passing adj. p < 0.05 & |log2FC| > 0.5
๐Ÿท๏ธ
Cell Types Compared
13
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.

๐Ÿ“‹ Top Marker Genes

๐Ÿ“ฅ Top Markers ๐Ÿ“ฅ All Significant DEGs ๐Ÿ“ฅ Full DEG Results
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
๐Ÿฅ

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

๐Ÿ”ฌ
Diseases Tested
15
Disease categories analyzed
โœ…
Significant Associations
15
Cell type-disease links (adj. p < 0.05)

Top Associated Diseases

Systemic lupus erythematosus Multiple sclerosis Multiple sclerosis Autism spectrum disorder Autism spectrum disorder
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.

๐Ÿ“ฅ Disease Enrichment Data
๐Ÿ“„

Full Analysis ReportComprehensive Summary & Downloads

๐Ÿ“Š

Interactive HTML Report

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

๐Ÿ“„ Open Report
๐Ÿ“ฆ

Download All Results

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

๐Ÿ“ฅ Download ZIP
๐Ÿ”—

Share Results

Use this permanent link to share these analysis results:

analysis.php?SP_ID=SP239&sysID=sys04

๐Ÿ“ Available Result Files

Analysis File Type Action
Cell Communication cellchat_heatmap.png Figure (PNG) ๐Ÿ” View
Cell Communication cellchat_network.png Figure (PNG) ๐Ÿ” View
Cell Communication cellchat_pathway_dotplot.png Figure (PNG) ๐Ÿ” View
Cell Communication cellchat_interactions.csv Data (CSV) ๐Ÿ“ฅ Download
Cell Communication cellchat_pathway_summary.csv Data (CSV) ๐Ÿ“ฅ Download
GRN Analysis grn_tf_heatmap.png Figure (PNG) ๐Ÿ” View
GRN Analysis grn_network.png Figure (PNG) ๐Ÿ” View
GRN Analysis grn_tf_activity.csv Data (CSV) ๐Ÿ“ฅ Download
GRN Analysis grn_tf_targets.csv Data (CSV) ๐Ÿ“ฅ Download
Co-expression coexp_dendrogram.png Figure (PNG) ๐Ÿ” View
Co-expression coexp_module_heatmap.png Figure (PNG) ๐Ÿ” View
Co-expression coexp_modules.csv Data (CSV) ๐Ÿ“ฅ Download
Co-expression coexp_eigengenes.csv Data (CSV) ๐Ÿ“ฅ Download
DEG Analysis deg_volcano.png Figure (PNG) ๐Ÿ” View
DEG Analysis deg_marker_heatmap.png Figure (PNG) ๐Ÿ” View
DEG Analysis deg_top_markers.csv Data (CSV) ๐Ÿ“ฅ Download
DEG Analysis deg_significant.csv Data (CSV) ๐Ÿ“ฅ Download
DEG Analysis deg_all_results.csv Data (CSV) ๐Ÿ“ฅ Download
Disease disease_heatmap.png Figure (PNG) ๐Ÿ” View
Disease disease_dotplot.png Figure (PNG) ๐Ÿ” View
Disease disease_enrichment.csv Data (CSV) ๐Ÿ“ฅ Download
Report sys04_analysis_report.html Report (HTML) ๐Ÿ“„ Open
Report sys04_summary.json Summary (JSON) ๐Ÿ“ฅ Download