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

Analysis Results sys05tis03

Published legacy analysis modules for the selected page.

Species: SP239
Tissue: sys05tis03
Generated: 2026-08-07 23:48
Modules: 5
๐Ÿ“Š Tissue Level
๐Ÿ“ก
8,369
Cell Interactions
๐Ÿงฌ
876
TF-Target Pairs
๐Ÿ“Š
1,893
Significant DEGs
๐ŸŽฏ
180
GO Terms
๐Ÿ›ค๏ธ
160
KEGG Pathways
๐Ÿ”—
30
Co-exp Modules
โš—๏ธ
โ€”
Metab. Pathways
๐Ÿฅ
19
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
8,369
Significant ligand-receptor pairs
๐Ÿ›ค๏ธ
Signaling Pathways
27
Unique pathways detected
๐Ÿ“ค
Top Sender
Fibroblasts
Most active signaling cell type
๐Ÿ“ฅ
Top Receiver
Mast 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
Parietal cells Parietal cells TGFB1 TGFBR1 TGFb 0.0007 0.0845 0.0001
Parietal cells CD8+ T cells TGFB1 TGFBR1 TGFb 0.0007 0.2009 0.0001
Parietal cells Enteroendocrine cells TGFB1 TGFBR1 TGFb 0.0007 0.1061 0.0001
Parietal cells Gastric stem cells TGFB1 TGFBR1 TGFb 0.0007 0.1177 0.0001
Parietal cells Surface mucous cells TGFB1 TGFBR1 TGFb 0.0007 0.0741 0.0001
Parietal cells CD4+ T cells TGFB1 TGFBR1 TGFb 0.0007 0.2253 0.0002
Parietal cells B cells TGFB1 TGFBR1 TGFb 0.0007 0.2902 0.0002
Parietal cells Chief cells TGFB1 TGFBR1 TGFb 0.0007 0.0484 0
Parietal cells DN T cells TGFB1 TGFBR1 TGFb 0.0007 0.2368 0.0002
Parietal cells Endothelial cells TGFB1 TGFBR1 TGFb 0.0007 0.1723 0.0001
Parietal cells Smooth muscle cells TGFB1 TGFBR1 TGFb 0.0007 0.2432 0.0002
Parietal cells Mast cells TGFB1 TGFBR1 TGFb 0.0007 0.217 0.0002
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
876
Significant regulatory relationships

Top Regulatory TFs

FOS 91 targets
FOXA1 89 targets
GATA4 72 targets
SOX9 72 targets
JUN 52 targets
GATA3 43 targets
TCF7 41 targets
RUNX1 39 targets
EGR1 38 targets
RUNX2 37 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
1,893
Genes passing adj. p < 0.05 & |log2FC| > 0.5
๐Ÿท๏ธ
Cell Types Compared
20
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
MS4A1 41.6426 9.5915 0 0 0.7063 0.0065 B cells
CD74 58.2735 9.0565 0 0 1 0.14 B cells
CD79B 24.5466 8.4357 0 0 0.4175 0.004 B cells
HLA-DRA 55.8221 8.0193 0 0 0.967 0.0657 B cells
CD79A 31.5231 7.6212 0 0 0.5388 0.0103 B cells
PLAAT5 25.5022 6.9637 0 0 0.4398 0.0137 B cells
BANK1 48.64 6.8434 0 0 0.8416 0.103 B cells
CD83 41.1793 6.6106 0 0 0.717 0.0331 B cells
HLA-DPA1 48.4681 6.5445 0 0 0.8523 0.0634 B cells
HLA-DPB1 47.4162 6.305 0 0 0.8408 0.0835 B cells
CD3D 66.4186 4.8875 0 0 0.8441 0.1294 CD4+ T cells
PTPRC 71.2933 4.8505 0 0 0.9582 0.2119 CD4+ T 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
19
Cell type-disease links (adj. p < 0.05)

Top Associated Diseases

Systemic lupus erythematosus Systemic lupus erythematosus Alzheimer disease Alzheimer disease Rheumatoid arthritis
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&tisID=sys05tis03

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 sys05tis03_analysis_report.html Report (HTML) ๐Ÿ“„ Open
Report sys05tis03_summary.json Summary (JSON) ๐Ÿ“ฅ Download