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 335
6
Diseases
10
Unique genes
0.260
Avg. similarity score
Benta disease
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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Benta disease
Congenital cardiovascular anomaly
immunodeficiency 11b with atopic dermatitis
severe combined immunodeficiency due to CARD11 deficiency
Osteopenia
Fanconi anemia complementation group C
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Benta disease | 4 | 4 | 1 |
| Congenital cardiovascular anomaly | 4 | 4 | 7 |
| immunodeficiency 11b with atopic dermatitis | 4 | 4 | 1 |
| severe combined immunodeficiency due to CARD11 deficiency | 4 | 4 | 1 |
| Osteopenia | 3 | 3 | 4 |
| Fanconi anemia complementation group C | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CARD11 | 5 / 6 | Benta disease, Congenital cardiovascular anomaly, immunodeficiency 11b with atopic dermatitis, Osteopenia and 1 more |
| FANCC | 2 / 6 | Congenital cardiovascular anomaly, Fanconi anemia complementation group C |
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 ⇵ |
|---|---|---|---|---|---|
| Parathyroid hormone synthesis, secretion and action | KEGG | 2 / 115 | 20.9× | 3.89e-3 | 3.70e-2 ✓ sig. |
| Misspliced LRP5 mutants have enhanced beta-catenin-dependent signaling | Reactome | 1 / 6 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Platelet Aggregation (Plug Formation) | Reactome | 1 / 8 | 150× | 6.64e-3 | 5.28e-2 |
| Negative regulation of TCF-dependent signaling by WNT ligand antagonists | Reactome | 1 / 8 | 150× | 6.64e-3 | 5.28e-2 |
| RNF mutants show enhanced WNT signaling and proliferation | Reactome | 1 / 8 | 150× | 6.64e-3 | 5.28e-2 |
| Platelet Adhesion to exposed collagen | Reactome | 1 / 11 | 109× | 9.12e-3 | 6.50e-2 |
| GP1b-IX-V activation signalling | Reactome | 1 / 12 | 100× | 9.95e-3 | 6.82e-2 |
| Interaction between L1 and Ankyrins | Reactome | 1 / 13 | 92.4× | 1.08e-2 | 7.19e-2 |
| Proteoglycans in cancer | KEGG | 2 / 204 | 11.8× | 1.18e-2 | 7.59e-2 |
| Extracellular matrix organization | Reactome | 1 / 15 | 80.1× | 1.24e-2 | 7.78e-2 |
| Anchoring fibril formation | Reactome | 1 / 15 | 80.1× | 1.24e-2 | 7.78e-2 |
| Crosslinking of collagen fibrils | Reactome | 1 / 18 | 66.7× | 1.49e-2 | 8.66e-2 |
| Cytoskeleton in muscle cells | KEGG | 2 / 232 | 10.4× | 1.51e-2 | 8.72e-2 |
| Regulation of FZD by ubiquitination | Reactome | 1 / 21 | 57.2× | 1.74e-2 | 9.50e-2 |
| Non-integrin membrane-ECM interactions | Reactome | 1 / 24 | 50.0× | 1.98e-2 | 1.02e-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 ⇵ |
|---|---|---|---|---|---|
| response to peptide hormone | GO:0043434 | 2 / 50 | 74.7× | 3.11e-4 | 6.90e-3 ✓ sig. |
| embryonic digit morphogenesis | GO:0042733 | 2 / 57 | 65.6× | 4.05e-4 | 8.28e-3 ✓ sig. |
| protein localization to T-tubule | GO:0036371 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| atrial cardiac muscle cell to AV node cell communication | GO:0086066 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| SA node cell to atrial cardiac muscle cell communication | GO:0086070 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| cellular response to vitamin E | GO:0071306 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| regulation of peptidyl-serine phosphorylation | GO:0033135 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| regulation of RNA polymerase II regulatory region sequence-specific DNA binding | GO:1903025 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| regulation of blood pressure | GO:0008217 | 2 / 83 | 45.0× | 8.57e-4 | 1.36e-2 ✓ sig. |
| protein localization to M-band | GO:0036309 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| cellular response to fluoride | GO:1902618 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| cell-cell signaling involved in mammary gland development | GO:0060764 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| tooth mineralization | GO:0034505 | 1 / 3 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| regulation of atrial cardiac muscle cell action potential | GO:0098910 | 1 / 3 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| mesodermal cell migration | GO:0008078 | 1 / 4 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |