Disease Clusters?
Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.
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Cluster 354
6
Diseases
7
Unique genes
0.286
Avg. similarity score
Congenital factor xiii deficiency
Most-connected disease (5 links)
Disease
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Congenital factor xiii deficiency
Factor xiii deficiency
Cholesteatoma
Coagulation factor deficiency syndrome
factor XIII, b subunit, deficiency of
factor XIII, A subunit, deficiency of
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital factor xiii deficiency | 5 | 5 | 2 |
| Factor xiii deficiency | 5 | 5 | 2 |
| Cholesteatoma | 4 | 4 | 5 |
| Coagulation factor deficiency syndrome | 4 | 4 | 2 |
| factor XIII, b subunit, deficiency of | 4 | 4 | 1 |
| factor XIII, A subunit, deficiency of | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| F13B | 5 / 6 | Cholesteatoma, Coagulation factor deficiency syndrome, Congenital factor xiii deficiency, Factor xiii deficiency and 1 more |
| F13A1 | 3 / 6 | Congenital factor xiii deficiency, Factor xiii deficiency, factor XIII, A subunit, deficiency of |
What do these columns mean?
- Connections in cluster
- How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
- Significant partners
- How many of those links are statistically significant (FDR q < 0.05).
- Curated genes
- Distinct curated genes linked to that disease in GeDiPNet.
- Member diseases (Top shared genes)
- How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
- Overlap genes (x / y)
- x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
- Cluster gene count
- Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
- Fold enrichment
- Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
- P-value / FDR q-value
- Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
- Shared genes (Pairs within this cluster)
- Number of curated genes the two diseases in that row have in common.
- Similarity score (Pairs within this cluster)
- Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.
Enriched Pathways (why this cluster is grouped, biologically)
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Complement and coagulation cascades | KEGG | 3 / 88 | 58.5× | 1.30e-5 | 4.18e-4 ✓ sig. |
| Common Pathway of Fibrin Clot Formation | Reactome | 2 / 22 | 156× | 6.69e-5 | 1.62e-3 ✓ sig. |
| Coronavirus disease - COVID-19 | KEGG | 3 / 238 | 21.6× | 2.54e-4 | 4.70e-3 ✓ sig. |
| RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) | Reactome | 1 / 10 | 172× | 5.82e-3 | 4.84e-2 ✓ sig. |
| Interleukin-2 signaling | Reactome | 1 / 12 | 143× | 6.97e-3 | 5.45e-2 |
| RORA activates gene expression | Reactome | 1 / 18 | 95.3× | 1.04e-2 | 7.05e-2 |
| Regulation of lipid metabolism by PPARalpha | Reactome | 1 / 20 | 85.8× | 1.16e-2 | 7.50e-2 |
| Intrinsic Pathway of Fibrin Clot Formation | Reactome | 1 / 23 | 74.6× | 1.33e-2 | 8.11e-2 |
| Interleukin receptor SHC signaling | Reactome | 1 / 27 | 63.5× | 1.56e-2 | 8.93e-2 |
| Notch-HLH transcription pathway | Reactome | 1 / 28 | 61.3× | 1.62e-2 | 9.12e-2 |
| Circadian Clock | Reactome | 1 / 28 | 61.3× | 1.62e-2 | 9.12e-2 |
| NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux | Reactome | 1 / 37 | 46.4× | 2.14e-2 | 1.07e-1 |
| Allograft rejection | KEGG | 1 / 39 | 44.0× | 2.25e-2 | 1.10e-1 |
| Activation of gene expression by SREBF (SREBP) | Reactome | 1 / 42 | 40.9× | 2.42e-2 | 1.15e-1 |
| Type I diabetes mellitus | KEGG | 1 / 44 | 39.0× | 2.54e-2 | 1.17e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| hemostasis | GO:0007599 | 3 / 55 | 146× | 8.37e-7 | 7.18e-5 ✓ sig. |
| blood coagulation, fibrin clot formation | GO:0072378 | 2 / 9 | 593× | 4.32e-6 | 2.67e-4 ✓ sig. |
| blood coagulation | GO:0007596 | 3 / 106 | 75.6× | 6.11e-6 | 3.52e-4 ✓ sig. |
| response to tacrolimus | GO:1901327 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| regulation of CD4-positive, alpha-beta T cell proliferation | GO:2000561 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| leukocyte activation involved in immune response | GO:0002366 | 1 / 3 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| regulation of T cell homeostatic proliferation | GO:0046013 | 1 / 3 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| positive regulation of plasma cell differentiation | GO:1900100 | 1 / 4 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| positive regulation of fibrinolysis | GO:0051919 | 1 / 4 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| positive regulation of tissue remodeling | GO:0034105 | 1 / 6 | 445× | 2.25e-3 | 2.41e-2 ✓ sig. |
| negative regulation of lymphocyte proliferation | GO:0050672 | 1 / 7 | 381× | 2.62e-3 | 2.62e-2 ✓ sig. |
| positive regulation of lymphocyte differentiation | GO:0045621 | 1 / 8 | 334× | 2.99e-3 | 2.82e-2 ✓ sig. |
| regulation of triglyceride metabolic process | GO:0090207 | 1 / 8 | 334× | 2.99e-3 | 2.82e-2 ✓ sig. |
| negative regulation of T-helper 17 cell differentiation | GO:2000320 | 1 / 9 | 297× | 3.37e-3 | 3.01e-2 ✓ sig. |
| fat pad development | GO:0060613 | 1 / 10 | 267× | 3.74e-3 | 3.18e-2 ✓ sig. |