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 145
9
Diseases
33
Unique genes
0.257
Avg. similarity score
Developmental venous anomaly
Most-connected disease (7 links)
Disease
Searched: Hydrops fetalis
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Hydrops fetalis
Developmental venous anomaly
Cavernous malformations of cns
Cerebral cavernous malformation
Congenital cerebral aneurysm
Congenital malformation of cerebral vessels
Hereditary hemorrhagic telangiectasia
Parkes weber syndrome
Angiokeratoma
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Developmental venous anomaly | 7 | 7 | 4 |
| Cavernous malformations of cns | 5 | 5 | 8 |
| Cerebral cavernous malformation | 5 | 5 | 6 |
| Congenital cerebral aneurysm | 4 | 4 | 2 |
| Congenital malformation of cerebral vessels | 4 | 4 | 2 |
| Hereditary hemorrhagic telangiectasia | 3 | 3 | 7 |
| Hydrops fetalis | 3 | 3 | 16 |
| Parkes weber syndrome | 3 | 3 | 3 |
| Angiokeratoma | 2 | 2 | 3 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CCM2 | 5 / 9 | Cavernous malformations of cns, Cerebral cavernous malformation, Congenital cerebral aneurysm, Congenital malformation of cerebral vessels and 1 more |
| PDCD10 | 5 / 9 | Cavernous malformations of cns, Cerebral cavernous malformation, Congenital cerebral aneurysm, Congenital malformation of cerebral vessels and 1 more |
| CCNH | 4 / 9 | Developmental venous anomaly, Hereditary hemorrhagic telangiectasia, Hydrops fetalis, Parkes weber syndrome |
| RASA1 | 4 / 9 | Developmental venous anomaly, Hereditary hemorrhagic telangiectasia, Hydrops fetalis, Parkes weber syndrome |
| KRIT1 | 3 / 9 | Angiokeratoma, Cavernous malformations of cns, Cerebral cavernous malformation |
| ANKIB1 | 2 / 9 | Angiokeratoma, Cavernous malformations of cns |
| PIK3CA | 2 / 9 | 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 ⇵ |
|---|---|---|---|---|---|
| Signaling by BMP | Reactome | 3 / 28 | 39.0× | 5.91e-5 | 1.48e-3 ✓ sig. |
| Adherens junction | KEGG | 4 / 93 | 15.7× | 1.16e-4 | 2.55e-3 ✓ sig. |
| Neurotrophin signaling pathway | KEGG | 4 / 120 | 12.1× | 3.10e-4 | 5.58e-3 ✓ sig. |
| Apelin signaling pathway | KEGG | 4 / 140 | 10.4× | 5.57e-4 | 8.84e-3 ✓ sig. |
| Signaling by cytosolic FGFR1 fusion mutants | Reactome | 2 / 18 | 40.4× | 1.09e-3 | 1.48e-2 ✓ sig. |
| Pancreatic cancer | KEGG | 3 / 77 | 14.2× | 1.20e-3 | 1.60e-2 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 3 / 77 | 14.2× | 1.20e-3 | 1.60e-2 ✓ sig. |
| Signal transduction by L1 | Reactome | 2 / 21 | 34.7× | 1.49e-3 | 1.89e-2 ✓ sig. |
| Colorectal cancer | KEGG | 3 / 87 | 12.5× | 1.71e-3 | 2.08e-2 ✓ sig. |
| PD-L1 expression and PD-1 checkpoint pathway in cancer | KEGG | 3 / 90 | 12.1× | 1.89e-3 | 2.23e-2 ✓ sig. |
| Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) | Reactome | 1 / 1 | 364× | 2.75e-3 | 2.95e-2 ✓ sig. |
| Downstream signal transduction | Reactome | 2 / 29 | 25.1× | 2.84e-3 | 3.01e-2 ✓ sig. |
| Human T-cell leukemia virus 1 infection | KEGG | 4 / 224 | 6.5× | 3.15e-3 | 3.23e-2 ✓ sig. |
| Signaling by FGFR1 in disease | Reactome | 2 / 33 | 22.1× | 3.67e-3 | 3.60e-2 ✓ sig. |
| Sterols are 12-hydroxylated by CYP8B1 | Reactome | 1 / 2 | 182× | 5.49e-3 | 4.75e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| angiogenesis | GO:0001525 | 8 / 284 | 16.0× | 2.58e-8 | 3.84e-6 ✓ sig. |
| venous blood vessel morphogenesis | GO:0048845 | 3 / 7 | 243× | 1.75e-7 | 1.96e-5 ✓ sig. |
| endothelium development | GO:0003158 | 3 / 10 | 170× | 5.97e-7 | 5.48e-5 ✓ sig. |
| negative regulation of endothelial cell proliferation | GO:0001937 | 4 / 39 | 58.1× | 6.34e-7 | 5.75e-5 ✓ sig. |
| positive regulation of SMAD protein signal transduction | GO:0060391 | 4 / 42 | 53.9× | 8.60e-7 | 7.41e-5 ✓ sig. |
| negative regulation of gene expression | GO:0010629 | 7 / 339 | 11.7× | 1.73e-6 | 1.30e-4 ✓ sig. |
| vasculogenesis | GO:0001570 | 4 / 63 | 36.0× | 4.46e-6 | 2.79e-4 ✓ sig. |
| activin receptor signaling pathway | GO:0032924 | 3 / 22 | 77.2× | 7.55e-6 | 4.27e-4 ✓ sig. |
| positive regulation of angiogenesis | GO:0045766 | 5 / 159 | 17.8× | 8.20e-6 | 4.56e-4 ✓ sig. |
| endocardial cushion to mesenchymal transition | GO:0090500 | 2 / 3 | 378× | 9.06e-6 | 4.93e-4 ✓ sig. |
| negative regulation of endothelial cell migration | GO:0010596 | 3 / 25 | 68.0× | 1.12e-5 | 5.79e-4 ✓ sig. |
| BMP signaling pathway | GO:0030509 | 4 / 88 | 25.7× | 1.69e-5 | 7.99e-4 ✓ sig. |
| cellular response to BMP stimulus | GO:0071773 | 3 / 33 | 51.5× | 2.64e-5 | 1.13e-3 ✓ sig. |
| blood vessel morphogenesis | GO:0048514 | 3 / 34 | 50.0× | 2.89e-5 | 1.20e-3 ✓ sig. |
| positive regulation of BMP signaling pathway | GO:0030513 | 3 / 40 | 42.5× | 4.74e-5 | 1.76e-3 ✓ sig. |