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 269
7
Diseases
7
Unique genes
0.290
Avg. similarity score
Bilateral perisylvian polymicrogyria
Most-connected disease (5 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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Bilateral perisylvian polymicrogyria
Combined immunodeficiency, enteropathy spectrum
Combined immunodeficiency-multiple intestinal atresia
Gastrointestinal defects and immunodeficiency syndrome
Heparin cofactor 2 deficiency
Multiple intestinal atresia
Bilateral frontoparietal polymicrogyria
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Bilateral perisylvian polymicrogyria | 5 | 5 | 3 |
| Combined immunodeficiency, enteropathy spectrum | 5 | 5 | 3 |
| Combined immunodeficiency-multiple intestinal atresia | 5 | 5 | 2 |
| Gastrointestinal defects and immunodeficiency syndrome | 5 | 5 | 3 |
| Heparin cofactor 2 deficiency | 4 | 4 | 3 |
| Multiple intestinal atresia | 3 | 3 | 1 |
| Bilateral frontoparietal polymicrogyria | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PI4KA | 5 / 7 | Bilateral perisylvian polymicrogyria, Combined immunodeficiency, enteropathy spectrum, Combined immunodeficiency-multiple intestinal atresia, Gastrointestinal defects and immunodeficiency syndrome and 1 more |
| TTC7A | 4 / 7 | Combined immunodeficiency, enteropathy spectrum, Combined immunodeficiency-multiple intestinal atresia, Gastrointestinal defects and immunodeficiency syndrome, Multiple intestinal atresia |
| ADGRG1 | 2 / 7 | Bilateral frontoparietal polymicrogyria, Bilateral perisylvian polymicrogyria |
| MCFD2 | 2 / 7 | Combined immunodeficiency, enteropathy spectrum, Gastrointestinal defects and immunodeficiency syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Transport to the Golgi and subsequent modification | Reactome | 1 / 2 | 858× | 1.17e-3 | 1.52e-2 ✓ sig. |
| Synthesis of PIPs at the ER membrane | Reactome | 1 / 5 | 343× | 2.91e-3 | 3.01e-2 ✓ sig. |
| Synthesis of PIPs at the Golgi membrane | Reactome | 1 / 18 | 95.3× | 1.04e-2 | 7.05e-2 |
| Common Pathway of Fibrin Clot Formation | Reactome | 1 / 22 | 78.0× | 1.28e-2 | 7.89e-2 |
| Intrinsic Pathway of Fibrin Clot Formation | Reactome | 1 / 23 | 74.6× | 1.33e-2 | 8.11e-2 |
| Cargo concentration in the ER | Reactome | 1 / 33 | 52.0× | 1.91e-2 | 1.00e-1 |
| COPII-mediated vesicle transport | Reactome | 1 / 68 | 25.2× | 3.90e-2 | 1.49e-1 |
| Viral myocarditis | KEGG | 1 / 70 | 24.5× | 4.01e-2 | 1.52e-1 |
| ISG15 antiviral mechanism | Reactome | 1 / 72 | 23.8× | 4.12e-2 | 1.54e-1 |
| Inositol phosphate metabolism | KEGG | 1 / 73 | 23.5× | 4.18e-2 | 1.55e-1 |
| Complement and coagulation cascades | KEGG | 1 / 88 | 19.5× | 5.02e-2 | 1.72e-1 |
| Phosphatidylinositol signaling system | KEGG | 1 / 98 | 17.5× | 5.58e-2 | 1.81e-1 |
| Post-translational protein phosphorylation | Reactome | 1 / 108 | 15.9× | 6.13e-2 | 1.90e-1 |
| Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | Reactome | 1 / 125 | 13.7× | 7.06e-2 | 2.06e-1 |
| Metabolic pathways | KEGG | 1 / 1,563 | 1.1× | 6.23e-1 | 7.47e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| phosphatidylinositol phosphate biosynthetic process | GO:0046854 | 2 / 43 | 124× | 1.08e-4 | 3.20e-3 ✓ sig. |
| reorganization of cellular membranes to establish viral sites of replication | GO:0140754 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| cerebral cortex radial glia-guided migration | GO:0021801 | 1 / 5 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| regulation of phosphorylation | GO:0042325 | 1 / 6 | 445× | 2.25e-3 | 2.41e-2 ✓ sig. |
| regulation of platelet aggregation | GO:0090330 | 1 / 7 | 381× | 2.62e-3 | 2.62e-2 ✓ sig. |
| cerebral cortex regionalization | GO:0021796 | 1 / 7 | 381× | 2.62e-3 | 2.62e-2 ✓ sig. |
| Rho-activating G protein-coupled receptor signaling pathway | GO:0160221 | 1 / 7 | 381× | 2.62e-3 | 2.62e-2 ✓ sig. |
| host-mediated perturbation of viral process | GO:0044788 | 1 / 8 | 334× | 2.99e-3 | 2.82e-2 ✓ sig. |
| negative regulation of neuron migration | GO:2001223 | 1 / 12 | 222× | 4.49e-3 | 3.47e-2 ✓ sig. |
| angiogenesis | GO:0001525 | 2 / 284 | 18.8× | 4.60e-3 | 3.53e-2 ✓ sig. |
| tube development | GO:0035295 | 1 / 13 | 205× | 4.86e-3 | 3.60e-2 ✓ sig. |
| negative regulation of ferroptosis | GO:0110076 | 1 / 14 | 191× | 5.23e-3 | 3.76e-2 ✓ sig. |
| positive regulation of vascular endothelial growth factor signaling pathway | GO:1900748 | 1 / 15 | 178× | 5.61e-3 | 3.88e-2 ✓ sig. |
| layer formation in cerebral cortex | GO:0021819 | 1 / 18 | 148× | 6.72e-3 | 4.27e-2 ✓ sig. |
| vocalization behavior | GO:0071625 | 1 / 19 | 141× | 7.10e-3 | 4.37e-2 ✓ sig. |