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 373
5
Diseases
4
Unique genes
0.302
Avg. similarity score
Corneal opacity
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Corneal opacity
Alagille syndrome
Deafness with congenital heart defects and posterior embryotoxon
Hepatic ductular hypoplasia
Proximal renal tubular acidosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Corneal opacity | 4 | 4 | 3 |
| Alagille syndrome | 3 | 3 | 2 |
| Deafness with congenital heart defects and posterior embryotoxon | 3 | 3 | 1 |
| Hepatic ductular hypoplasia | 3 | 3 | 1 |
| Proximal renal tubular acidosis | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| JAG1 | 4 / 5 | Alagille syndrome, Corneal opacity, Deafness with congenital heart defects and posterior embryotoxon, Hepatic ductular hypoplasia |
| SLC4A4 | 2 / 5 | Corneal opacity, Proximal renal tubular acidosis |
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 ⇵ |
|---|---|---|---|---|---|
| Notch signaling pathway | KEGG | 2 / 62 | 96.9× | 1.56e-4 | 3.21e-3 ✓ sig. |
| MPS IV - Morquio syndrome B | Reactome | 1 / 1 | 3,003× | 3.33e-4 | 5.82e-3 ✓ sig. |
| Defective SLC4A4 causes renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) | Reactome | 1 / 1 | 3,003× | 3.33e-4 | 5.82e-3 ✓ sig. |
| Th1 and Th2 cell differentiation | KEGG | 2 / 93 | 64.6× | 3.52e-4 | 6.09e-3 ✓ sig. |
| Endocrine resistance | KEGG | 2 / 99 | 60.7× | 3.99e-4 | 6.70e-3 ✓ sig. |
| Breast cancer | KEGG | 2 / 148 | 40.6× | 8.90e-4 | 1.24e-2 ✓ sig. |
| Defective NEU1 causes sialidosis | Reactome | 1 / 3 | 1,001× | 9.99e-4 | 1.35e-2 ✓ sig. |
| NOTCH2 Activation and Transmission of Signal to the Nucleus | Reactome | 1 / 3 | 1,001× | 9.99e-4 | 1.35e-2 ✓ sig. |
| Defective LFNG causes SCDO3 | Reactome | 1 / 5 | 601× | 1.66e-3 | 2.00e-2 ✓ sig. |
| Chemical carcinogenesis - receptor activation | KEGG | 2 / 215 | 27.9× | 1.87e-3 | 2.17e-2 ✓ sig. |
| Pre-NOTCH Processing in Golgi | Reactome | 1 / 6 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| NOTCH2 intracellular domain regulates transcription | Reactome | 1 / 7 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant | Reactome | 1 / 7 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| Bicarbonate transporters | Reactome | 1 / 10 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| Keratan sulfate degradation | Reactome | 1 / 13 | 231× | 4.32e-3 | 3.98e-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 ⇵ |
|---|---|---|---|---|---|
| ciliary body morphogenesis | GO:0061073 | 2 / 4 | 2,336× | 2.06e-7 | 2.23e-5 ✓ sig. |
| podocyte development | GO:0072015 | 2 / 9 | 1,038× | 1.24e-6 | 9.83e-5 ✓ sig. |
| morphogenesis of an epithelial sheet | GO:0002011 | 2 / 10 | 934× | 1.55e-6 | 1.17e-4 ✓ sig. |
| cardiac septum morphogenesis | GO:0060411 | 2 / 16 | 584× | 4.12e-6 | 2.57e-4 ✓ sig. |
| cell fate determination | GO:0001709 | 2 / 18 | 519× | 5.25e-6 | 3.12e-4 ✓ sig. |
| pulmonary valve morphogenesis | GO:0003184 | 2 / 18 | 519× | 5.25e-6 | 3.12e-4 ✓ sig. |
| hemopoiesis | GO:0030097 | 2 / 89 | 105× | 1.34e-4 | 3.76e-3 ✓ sig. |
| endocardial cushion cell development | GO:0061444 | 1 / 1 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| response to cortisone | GO:0051413 | 1 / 1 | 4,672× | 2.14e-4 | 5.28e-3 ✓ sig. |
| Notch signaling pathway | GO:0007219 | 2 / 117 | 79.9× | 2.31e-4 | 5.59e-3 ✓ sig. |
| animal organ morphogenesis | GO:0009887 | 2 / 130 | 71.9× | 2.86e-4 | 6.47e-3 ✓ sig. |
| cholangiocyte proliferation | GO:1990705 | 1 / 2 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| intrahepatic bile duct development | GO:0035622 | 1 / 2 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| keratan sulfate proteoglycan catabolic process | GO:0042340 | 1 / 2 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| response to Thyroglobulin triiodothyronine | GO:1904016 | 1 / 2 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Deafness with congenital heart defects and posterior embryotoxon | Hepatic ductular hypoplasia | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Alagille syndrome | Deafness with congenital heart defects and posterior embryotoxon | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Alagille syndrome | Hepatic ductular hypoplasia | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Corneal opacity | Deafness with congenital heart defects and posterior embryotoxon | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Corneal opacity | Hepatic ductular hypoplasia | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Corneal opacity | Proximal renal tubular acidosis | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Alagille syndrome | Corneal opacity | 0.200 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |