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 408
5
Diseases
4
Unique genes
0.361
Avg. similarity score
Congenital factor ii deficiency
Most-connected disease (4 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Congenital factor ii deficiency
Congenital prothrombin deficiency
thrombophilia due to thrombin defect
Cerebral sinovenous thrombosis
Hemophilia b
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital factor ii deficiency | 4 | 4 | 1 |
| Congenital prothrombin deficiency | 4 | 4 | 1 |
| thrombophilia due to thrombin defect | 4 | 4 | 1 |
| Cerebral sinovenous thrombosis | 3 | 3 | 3 |
| Hemophilia b | 3 | 3 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| F2 | 5 / 5 | Cerebral sinovenous thrombosis, Congenital factor ii deficiency, Congenital prothrombin deficiency, Hemophilia b 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)
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 | 4 / 55 | 340× | 6.71e-11 | 2.00e-8 ✓ sig. |
| blood coagulation | GO:0007596 | 4 / 106 | 176× | 9.78e-10 | 2.20e-7 ✓ sig. |
| proteolysis | GO:0006508 | 3 / 613 | 22.9× | 1.37e-4 | 3.82e-3 ✓ sig. |
| response to vitamin K | GO:0032571 | 1 / 3 | 1,557× | 6.42e-4 | 1.13e-2 ✓ sig. |
| neutrophil-mediated killing of gram-negative bacterium | GO:0070945 | 1 / 5 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| regulation of body fluid levels | GO:0050878 | 1 / 7 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway | GO:1900738 | 1 / 7 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| negative regulation of platelet activation | GO:0010544 | 1 / 9 | 519× | 1.93e-3 | 2.20e-2 ✓ sig. |
| cytolysis by host of symbiont cells | GO:0051838 | 1 / 11 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| ligand-gated ion channel signaling pathway | GO:1990806 | 1 / 11 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| negative regulation of astrocyte differentiation | GO:0048712 | 1 / 11 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| thrombin-activated receptor signaling pathway | GO:0070493 | 1 / 11 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| regulation of blood coagulation | GO:0030193 | 1 / 11 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| negative regulation of fibrinolysis | GO:0051918 | 1 / 12 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| positive regulation of blood coagulation | GO:0030194 | 1 / 15 | 311× | 3.21e-3 | 2.91e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital factor ii deficiency | Congenital prothrombin deficiency | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital factor ii deficiency | thrombophilia due to thrombin defect | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital prothrombin deficiency | thrombophilia due to thrombin defect | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital factor ii deficiency | Hemophilia b | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Congenital prothrombin deficiency | Hemophilia b | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Hemophilia b | thrombophilia due to thrombin defect | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Cerebral sinovenous thrombosis | Congenital factor ii deficiency | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Cerebral sinovenous thrombosis | Congenital prothrombin deficiency | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Cerebral sinovenous thrombosis | thrombophilia due to thrombin defect | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |