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 566
5
Diseases
3
Unique genes
0.400
Avg. similarity score
Bietti crystalline corneoretinal dystrophy
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Bietti crystalline corneoretinal dystrophy
Coagulation disorder
Congenital prekallikrein deficiency
Fletcher factor (prekallikrein) deficiency
Inherited prekallikrein deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bietti crystalline corneoretinal dystrophy | 4 | 4 | 3 |
| Coagulation disorder | 4 | 4 | 1 |
| Congenital prekallikrein deficiency | 4 | 4 | 1 |
| Fletcher factor (prekallikrein) deficiency | 4 | 4 | 1 |
| Inherited prekallikrein deficiency | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| KLKB1 | 5 / 5 | Bietti crystalline corneoretinal dystrophy, Coagulation disorder, Congenital prekallikrein deficiency, Fletcher factor (prekallikrein) deficiency and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| The canonical retinoid cycle in rods (twilight vision) | Reactome | 2 / 20 | 400× | 7.90e-6 | 2.40e-4 ✓ sig. |
| Retinoid cycle disease events | Reactome | 1 / 13 | 308× | 3.24e-3 | 2.69e-2 ✓ sig. |
| Intrinsic Pathway of Fibrin Clot Formation | Reactome | 1 / 23 | 174× | 5.73e-3 | 4.00e-2 ✓ sig. |
| Endogenous sterols | Reactome | 1 / 25 | 160× | 6.23e-3 | 4.21e-2 ✓ sig. |
| Activation of Matrix Metalloproteinases | Reactome | 1 / 33 | 121× | 8.22e-3 | 5.04e-2 |
| ABC transporters | KEGG | 1 / 45 | 89.0× | 1.12e-2 | 6.10e-2 |
| ABC-family proteins mediated transport | Reactome | 1 / 81 | 49.4× | 2.01e-2 | 8.59e-2 |
| Complement and coagulation cascades | KEGG | 1 / 88 | 45.5× | 2.18e-2 | 9.01e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| retinoid metabolic process | GO:0001523 | 2 / 38 | 328× | 1.21e-5 | 6.29e-4 ✓ sig. |
| Factor XII activation | GO:0002542 | 1 / 2 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| visual perception | GO:0007601 | 2 / 215 | 57.9× | 3.92e-4 | 8.07e-3 ✓ sig. |
| organic hydroxy compound transport | GO:0015850 | 1 / 3 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| phospholipid transfer to membrane | GO:0006649 | 1 / 3 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| retinol transport | GO:0034633 | 1 / 3 | 2,076× | 4.82e-4 | 9.24e-3 ✓ sig. |
| positive regulation of fibrinolysis | GO:0051919 | 1 / 4 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| fatty acid omega-oxidation | GO:0010430 | 1 / 6 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| plasminogen activation | GO:0031639 | 1 / 12 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
| phototransduction, visible light | GO:0007603 | 1 / 13 | 479× | 2.09e-3 | 2.17e-2 ✓ sig. |
| retinal metabolic process | GO:0042574 | 1 / 19 | 328× | 3.05e-3 | 2.62e-2 ✓ sig. |
| fibrinolysis | GO:0042730 | 1 / 19 | 328× | 3.05e-3 | 2.62e-2 ✓ sig. |
| sterol metabolic process | GO:0016125 | 1 / 22 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| phospholipid translocation | GO:0045332 | 1 / 27 | 231× | 4.33e-3 | 3.11e-2 ✓ sig. |
| zymogen activation | GO:0031638 | 1 / 32 | 195× | 5.13e-3 | 3.37e-2 ✓ sig. |