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 134
10
Diseases
18
Unique genes
0.267
Avg. similarity score
Branchiootorenal syndrome
Most-connected disease (8 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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Branchiootorenal syndrome
Branchiootic syndrome
Asymmetric crying face association
Bor syndrome
Branchiooculofacial syndrome
Otofaciocervical syndrome
Cayler cardiofacial syndrome
Congenital abnormalities
otofaciocervical syndrome 2
Usher syndrome type 3
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Branchiootorenal syndrome | 8 | 8 | 7 |
| Branchiootic syndrome | 7 | 7 | 2 |
| Asymmetric crying face association | 6 | 6 | 1 |
| Bor syndrome | 6 | 6 | 3 |
| Branchiooculofacial syndrome | 6 | 6 | 2 |
| Otofaciocervical syndrome | 6 | 6 | 2 |
| Cayler cardiofacial syndrome | 5 | 5 | 1 |
| Congenital abnormalities | 3 | 3 | 13 |
| otofaciocervical syndrome 2 | 2 | 2 | 1 |
| Usher syndrome type 3 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| EYA1 | 8 / 10 | Asymmetric crying face association, Bor syndrome, Branchiooculofacial syndrome, Branchiootic syndrome and 4 more |
| SIX1 | 4 / 10 | Bor syndrome, Branchiootic syndrome, Branchiootorenal syndrome, Congenital abnormalities |
| PAX1 | 3 / 10 | Branchiootorenal syndrome, Otofaciocervical syndrome, otofaciocervical syndrome 2 |
| CLRN1 | 2 / 10 | Branchiootorenal syndrome, Usher syndrome type 3 |
| SIX5 | 2 / 10 | Bor syndrome, Branchiootorenal syndrome |
| TFAP2A | 2 / 10 | Branchiooculofacial syndrome, Branchiootorenal 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)
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| positive regulation of secondary heart field cardioblast proliferation | GO:0072513 | 2 / 3 | 692× | 2.63e-6 | 1.79e-4 ✓ sig. |
| compartment pattern specification | GO:0007386 | 2 / 4 | 519× | 5.25e-6 | 3.12e-4 ✓ sig. |
| ureteric bud development | GO:0001657 | 3 / 41 | 76.0× | 7.82e-6 | 4.30e-4 ✓ sig. |
| branching involved in ureteric bud morphogenesis | GO:0001658 | 3 / 45 | 69.2× | 1.04e-5 | 5.37e-4 ✓ sig. |
| sensory perception of sound | GO:0007605 | 4 / 162 | 25.6× | 1.51e-5 | 7.24e-4 ✓ sig. |
| negative regulation of DNA-templated transcription | GO:0045892 | 6 / 631 | 9.9× | 1.90e-5 | 8.61e-4 ✓ sig. |
| negative regulation of transcription by RNA polymerase II | GO:0000122 | 7 / 1,002 | 7.3× | 2.36e-5 | 1.02e-3 ✓ sig. |
| otic vesicle development | GO:0071599 | 2 / 8 | 260× | 2.45e-5 | 1.05e-3 ✓ sig. |
| outflow tract morphogenesis | GO:0003151 | 3 / 63 | 49.4× | 2.87e-5 | 1.18e-3 ✓ sig. |
| inner ear morphogenesis | GO:0042472 | 3 / 65 | 47.9× | 3.16e-5 | 1.27e-3 ✓ sig. |
| regulation of cell population proliferation | GO:0042127 | 4 / 201 | 20.7× | 3.53e-5 | 1.39e-3 ✓ sig. |
| positive regulation of DNA-templated transcription | GO:0045893 | 6 / 778 | 8.0× | 6.17e-5 | 2.10e-3 ✓ sig. |
| epidermal cell differentiation | GO:0009913 | 2 / 13 | 160× | 6.79e-5 | 2.26e-3 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 7 / 1,208 | 6.0× | 7.84e-5 | 2.52e-3 ✓ sig. |
| negative regulation of stem cell differentiation | GO:2000737 | 2 / 18 | 115× | 1.33e-4 | 3.74e-3 ✓ sig. |