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 414
5
Diseases
19
Unique genes
0.151
Avg. similarity score
Von willebrand disorder
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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Von willebrand disorder
Coronary thrombosis
Glycoprotein vi deficiency
platelet-type bleeding disorder 11
platelet-type bleeding disorder 8
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Von willebrand disorder | 4 | 4 | 9 |
| Coronary thrombosis | 3 | 3 | 12 |
| Glycoprotein vi deficiency | 3 | 3 | 1 |
| platelet-type bleeding disorder 11 | 3 | 3 | 1 |
| platelet-type bleeding disorder 8 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GP6 | 4 / 5 | Coronary thrombosis, Glycoprotein vi deficiency, platelet-type bleeding disorder 11, Von willebrand disorder |
| P2RY12 | 2 / 5 | platelet-type bleeding disorder 8, Von willebrand disorder |
| PLAT | 2 / 5 | Coronary thrombosis, Von willebrand disorder |
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 ⇵ |
|---|---|---|---|---|---|
| Platelet activation | KEGG | 7 / 126 | 35.1× | 5.37e-10 | 6.47e-8 ✓ sig. |
| ECM-receptor interaction | KEGG | 6 / 89 | 42.6× | 3.51e-9 | 3.44e-7 ✓ sig. |
| Platelet Adhesion to exposed collagen | Reactome | 3 / 11 | 172× | 5.49e-7 | 2.91e-5 ✓ sig. |
| p130Cas linkage to MAPK signaling for integrins | Reactome | 3 / 15 | 126× | 1.51e-6 | 6.95e-5 ✓ sig. |
| GRB2:SOS provides linkage to MAPK signaling for Integrins | Reactome | 3 / 15 | 126× | 1.51e-6 | 6.95e-5 ✓ sig. |
| Integrin signaling | Reactome | 3 / 23 | 82.4× | 5.83e-6 | 2.15e-4 ✓ sig. |
| Integrin cell surface interactions | Reactome | 4 / 81 | 31.2× | 6.89e-6 | 2.46e-4 ✓ sig. |
| Hematopoietic cell lineage | KEGG | 4 / 100 | 25.3× | 1.59e-5 | 4.95e-4 ✓ sig. |
| Signaling by high-kinase activity BRAF mutants | Reactome | 3 / 36 | 52.7× | 2.32e-5 | 6.74e-4 ✓ sig. |
| MAP2K and MAPK activation | Reactome | 3 / 40 | 47.4× | 3.20e-5 | 8.81e-4 ✓ sig. |
| Signaling by moderate kinase activity BRAF mutants | Reactome | 3 / 47 | 40.3× | 5.21e-5 | 1.32e-3 ✓ sig. |
| Paradoxical activation of RAF signaling by kinase inactive BRAF | Reactome | 3 / 47 | 40.3× | 5.21e-5 | 1.32e-3 ✓ sig. |
| Signaling downstream of RAS mutants | Reactome | 3 / 47 | 40.3× | 5.21e-5 | 1.32e-3 ✓ sig. |
| Platelet Aggregation (Plug Formation) | Reactome | 2 / 8 | 158× | 6.60e-5 | 1.60e-3 ✓ sig. |
| ECM proteoglycans | Reactome | 3 / 51 | 37.2× | 6.66e-5 | 1.61e-3 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| blood coagulation | GO:0007596 | 8 / 106 | 74.2× | 5.88e-14 | 3.38e-11 ✓ sig. |
| hemostasis | GO:0007599 | 5 / 55 | 89.4× | 2.07e-9 | 4.25e-7 ✓ sig. |
| platelet activation | GO:0030168 | 5 / 69 | 71.3× | 6.62e-9 | 1.20e-6 ✓ sig. |
| positive regulation of leukocyte migration | GO:0002687 | 3 / 19 | 155× | 8.55e-7 | 7.29e-5 ✓ sig. |
| cell-substrate adhesion | GO:0031589 | 3 / 25 | 118× | 2.02e-6 | 1.45e-4 ✓ sig. |
| cell adhesion | GO:0007155 | 7 / 665 | 10.4× | 2.43e-6 | 1.68e-4 ✓ sig. |
| collagen-activated signaling pathway | GO:0038065 | 2 / 6 | 328× | 1.47e-5 | 7.04e-4 ✓ sig. |
| platelet aggregation | GO:0070527 | 3 / 49 | 60.2× | 1.59e-5 | 7.54e-4 ✓ sig. |
| smooth muscle cell migration | GO:0014909 | 2 / 9 | 219× | 3.51e-5 | 1.38e-3 ✓ sig. |
| positive regulation of positive chemotaxis | GO:0050927 | 2 / 11 | 179× | 5.36e-5 | 1.89e-3 ✓ sig. |
| mesodermal cell differentiation | GO:0048333 | 2 / 13 | 151× | 7.59e-5 | 2.47e-3 ✓ sig. |
| positive regulation of cell adhesion mediated by integrin | GO:0033630 | 2 / 16 | 123× | 1.17e-4 | 3.40e-3 ✓ sig. |
| dendrite self-avoidance | GO:0070593 | 2 / 16 | 123× | 1.17e-4 | 3.40e-3 ✓ sig. |
| positive regulation of smooth muscle cell migration | GO:0014911 | 2 / 17 | 116× | 1.32e-4 | 3.73e-3 ✓ sig. |
| integrin-mediated signaling pathway | GO:0007229 | 3 / 100 | 29.5× | 1.35e-4 | 3.79e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Coronary thrombosis | Von willebrand disorder | 0.100 | 2 | 2.00e-5 | 1.00e-4 ✓ sig. |
| Glycoprotein vi deficiency | platelet-type bleeding disorder 11 | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Glycoprotein vi deficiency | Von willebrand disorder | 0.100 | 1 | 5.84e-4 | 1.14e-3 ✓ sig. |
| platelet-type bleeding disorder 11 | Von willebrand disorder | 0.100 | 1 | 5.84e-4 | 1.14e-3 ✓ sig. |
| platelet-type bleeding disorder 8 | Von willebrand disorder | 0.100 | 1 | 5.84e-4 | 1.14e-3 ✓ sig. |
| Coronary thrombosis | Glycoprotein vi deficiency | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Coronary thrombosis | platelet-type bleeding disorder 11 | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |