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 249
7
Diseases
13
Unique genes
0.275
Avg. similarity score
Cavernous malformations of cns
Most-connected disease (6 links)
Disease
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Cavernous malformations of cns
Cerebral cavernous malformation
Congenital cerebral aneurysm
Congenital malformation of cerebral vessels
Developmental venous anomaly
cerebral cavernous malformation 2
Angiokeratoma
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cavernous malformations of cns | 6 | 6 | 8 |
| Cerebral cavernous malformation | 6 | 6 | 6 |
| Congenital cerebral aneurysm | 5 | 5 | 2 |
| Congenital malformation of cerebral vessels | 5 | 5 | 2 |
| Developmental venous anomaly | 5 | 5 | 4 |
| cerebral cavernous malformation 2 | 5 | 5 | 1 |
| Angiokeratoma | 2 | 2 | 3 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CCM2 | 6 / 7 | Cavernous malformations of cns, Cerebral cavernous malformation, cerebral cavernous malformation 2, Congenital cerebral aneurysm and 2 more |
| PDCD10 | 5 / 7 | Cavernous malformations of cns, Cerebral cavernous malformation, Congenital cerebral aneurysm, Congenital malformation of cerebral vessels and 1 more |
| KRIT1 | 3 / 7 | Angiokeratoma, Cavernous malformations of cns, Cerebral cavernous malformation |
| ANKIB1 | 2 / 7 | Angiokeratoma, Cavernous malformations of cns |
| PIK3CA | 2 / 7 | Cavernous malformations of cns, Cerebral cavernous malformation |
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 ⇵ |
|---|---|---|---|---|---|
| Adherens junction | KEGG | 3 / 93 | 29.8× | 1.22e-4 | 2.62e-3 ✓ sig. |
| Downstream signal transduction | Reactome | 2 / 29 | 63.7× | 4.32e-4 | 7.11e-3 ✓ sig. |
| Sterols are 12-hydroxylated by CYP8B1 | Reactome | 1 / 2 | 462× | 2.16e-3 | 2.42e-2 ✓ sig. |
| PD-L1 expression and PD-1 checkpoint pathway in cancer | KEGG | 2 / 90 | 20.5× | 4.11e-3 | 3.84e-2 ✓ sig. |
| Synthesis of 5-eicosatetraenoic acids | Reactome | 1 / 6 | 154× | 6.48e-3 | 5.19e-2 |
| MET activates PI3K/AKT signaling | Reactome | 1 / 6 | 154× | 6.48e-3 | 5.19e-2 |
| IRS-mediated signalling | Reactome | 1 / 6 | 154× | 6.48e-3 | 5.19e-2 |
| Neurotrophin signaling pathway | KEGG | 2 / 120 | 15.4× | 7.19e-3 | 5.56e-2 |
| PI3K/AKT activation | Reactome | 1 / 9 | 103× | 9.70e-3 | 6.74e-2 |
| PI3K events in ERBB4 signaling | Reactome | 1 / 10 | 92.4× | 1.08e-2 | 7.19e-2 |
| Signaling by FGFR3 fusions in cancer | Reactome | 1 / 10 | 92.4× | 1.08e-2 | 7.19e-2 |
| Signaling by FGFR4 in disease | Reactome | 1 / 11 | 84.0× | 1.18e-2 | 7.60e-2 |
| Costimulation by the CD28 family | Reactome | 1 / 11 | 84.0× | 1.18e-2 | 7.60e-2 |
| Synthesis of Prostaglandins (PG) and Thromboxanes (TX) | Reactome | 1 / 12 | 77.0× | 1.29e-2 | 7.95e-2 |
| Eicosanoids | Reactome | 1 / 12 | 77.0× | 1.29e-2 | 7.95e-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 ⇵ |
|---|---|---|---|---|---|
| endothelium development | GO:0003158 | 3 / 10 | 431× | 3.15e-8 | 4.57e-6 ✓ sig. |
| regulation of angiogenesis | GO:0045765 | 3 / 43 | 100× | 3.19e-6 | 2.10e-4 ✓ sig. |
| angiogenesis | GO:0001525 | 4 / 284 | 20.2× | 3.35e-5 | 1.33e-3 ✓ sig. |
| negative regulation of nitric oxide biosynthetic process | GO:0045019 | 2 / 15 | 192× | 4.67e-5 | 1.71e-3 ✓ sig. |
| vasculature development | GO:0001944 | 2 / 33 | 87.1× | 2.33e-4 | 5.62e-3 ✓ sig. |
| organophosphate catabolic process | GO:0046434 | 1 / 1 | 1,437× | 6.96e-4 | 1.19e-2 ✓ sig. |
| response to butyrate | GO:1903544 | 1 / 1 | 1,437× | 6.96e-4 | 1.19e-2 ✓ sig. |
| vasculogenesis | GO:0001570 | 2 / 63 | 45.6× | 8.52e-4 | 1.36e-2 ✓ sig. |
| blood vessel development | GO:0001568 | 2 / 70 | 41.1× | 1.05e-3 | 1.56e-2 ✓ sig. |
| negative regulation of nitric-oxide synthase activity | GO:0051001 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| response to muscle inactivity | GO:0014870 | 1 / 2 | 719× | 1.39e-3 | 1.84e-2 ✓ sig. |
| glycosylceramide catabolic process | GO:0046477 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| cellular response to hydrostatic pressure | GO:0071464 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| negative regulation of plasma lipoprotein oxidation | GO:0034445 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |
| intrinsic apoptotic signaling pathway in response to hydrogen peroxide | GO:0036481 | 1 / 3 | 479× | 2.09e-3 | 2.31e-2 ✓ sig. |