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 210
8
Diseases
11
Unique genes
0.331
Avg. similarity score
Clouston syndrome
Most-connected disease (5 links)
Disease
Searched: ichthyosiform erythroderma, corneal involvement, and hearing loss
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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ichthyosiform erythroderma, corneal involvement, and hearing loss
Clouston syndrome
Deafness, x-linked
Hearing loss with stapes fixation
Keratitis-ichthyosis-deafness syndrome
Senter syndrome
X-linked hearing loss with perilymphatic gusher
X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Clouston syndrome | 5 | 5 | 1 |
| Deafness, x-linked | 5 | 5 | 10 |
| Hearing loss with stapes fixation | 5 | 5 | 3 |
| Keratitis-ichthyosis-deafness syndrome | 5 | 5 | 3 |
| Senter syndrome | 5 | 5 | 2 |
| X-linked hearing loss with perilymphatic gusher | 5 | 5 | 3 |
| X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism syndrome | 1 | 1 | 1 |
| ichthyosiform erythroderma, corneal involvement, and hearing loss | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GJB6 | 6 / 8 | Clouston syndrome, Deafness, x-linked, Hearing loss with stapes fixation, Keratitis-ichthyosis-deafness syndrome and 2 more |
| GJB2 | 5 / 8 | Deafness, x-linked, Hearing loss with stapes fixation, Keratitis-ichthyosis-deafness syndrome, Senter syndrome and 1 more |
| POU3F4 | 3 / 8 | Deafness, x-linked, Hearing loss with stapes fixation, X-linked hearing loss with perilymphatic gusher |
| AP1B1 | 2 / 8 | ichthyosiform erythroderma, corneal involvement, and hearing loss, Keratitis-ichthyosis-deafness syndrome |
| GPRASP2 | 2 / 8 | Deafness, x-linked, X-linked external auditory canal atresia, dilated internal auditory canal, facial dysmorphism 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 of connexons to the plasma membrane | Reactome | 1 / 1 | 1,092× | 9.16e-4 | 1.31e-2 ✓ sig. |
| 5-Phosphoribose 1-diphosphate biosynthesis | Reactome | 1 / 3 | 364× | 2.75e-3 | 2.97e-2 ✓ sig. |
| Nef mediated downregulation of MHC class I complex cell surface expression | Reactome | 1 / 10 | 109× | 9.12e-3 | 6.71e-2 |
| Extracellular matrix organization | Reactome | 1 / 15 | 72.8× | 1.37e-2 | 8.55e-2 |
| Anchoring fibril formation | Reactome | 1 / 15 | 72.8× | 1.37e-2 | 8.55e-2 |
| Gap junction assembly | Reactome | 1 / 18 | 60.7× | 1.64e-2 | 9.53e-2 |
| Crosslinking of collagen fibrils | Reactome | 1 / 18 | 60.7× | 1.64e-2 | 9.53e-2 |
| Non-integrin membrane-ECM interactions | Reactome | 1 / 24 | 45.5× | 2.18e-2 | 1.12e-1 |
| Laminin interactions | Reactome | 1 / 28 | 39.0× | 2.54e-2 | 1.22e-1 |
| Pentose phosphate pathway | KEGG | 1 / 31 | 35.2× | 2.80e-2 | 1.29e-1 |
| Lysosome Vesicle Biogenesis | Reactome | 1 / 35 | 31.2× | 3.16e-2 | 1.38e-1 |
| Collagen chain trimerization | Reactome | 1 / 44 | 24.8× | 3.96e-2 | 1.56e-1 |
| TBC/RABGAPs | Reactome | 1 / 46 | 23.7× | 4.14e-2 | 1.59e-1 |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 1 / 51 | 21.4× | 4.58e-2 | 1.68e-1 |
| Collagen degradation | Reactome | 1 / 52 | 21.0× | 4.66e-2 | 1.70e-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 ⇵ |
|---|---|---|---|---|---|
| gap junction-mediated intercellular transport | GO:1990349 | 2 / 6 | 566× | 4.72e-6 | 2.95e-4 ✓ sig. |
| cell communication by electrical coupling | GO:0010644 | 2 / 7 | 485× | 6.60e-6 | 3.88e-4 ✓ sig. |
| gap junction assembly | GO:0016264 | 2 / 8 | 425× | 8.80e-6 | 4.90e-4 ✓ sig. |
| sensory perception of sound | GO:0007605 | 3 / 162 | 31.5× | 1.00e-4 | 3.14e-3 ✓ sig. |
| hematopoietic stem cell homeostasis | GO:0061484 | 2 / 30 | 113× | 1.36e-4 | 3.92e-3 ✓ sig. |
| cell communication | GO:0007154 | 2 / 80 | 42.5× | 9.71e-4 | 1.53e-2 ✓ sig. |
| urate biosynthetic process | GO:0034418 | 1 / 2 | 849× | 1.18e-3 | 1.72e-2 ✓ sig. |
| hypoxanthine biosynthetic process | GO:0046101 | 1 / 2 | 849× | 1.18e-3 | 1.72e-2 ✓ sig. |
| protein import into mitochondrial intermembrane space | GO:0045041 | 1 / 3 | 566× | 1.76e-3 | 2.17e-2 ✓ sig. |
| mitochondrial disulfide relay system | GO:0160203 | 1 / 3 | 566× | 1.76e-3 | 2.17e-2 ✓ sig. |
| ribonucleoside monophosphate biosynthetic process | GO:0009156 | 1 / 4 | 425× | 2.35e-3 | 2.56e-2 ✓ sig. |
| basolateral protein secretion | GO:0110010 | 1 / 5 | 340× | 2.94e-3 | 2.90e-2 ✓ sig. |
| ear morphogenesis | GO:0042471 | 1 / 5 | 340× | 2.94e-3 | 2.90e-2 ✓ sig. |
| 5-phosphoribose 1-diphosphate biosynthetic process | GO:0006015 | 1 / 5 | 340× | 2.94e-3 | 2.90e-2 ✓ sig. |
| negative regulation of mesenchymal cell apoptotic process | GO:2001054 | 1 / 6 | 283× | 3.53e-3 | 3.16e-2 ✓ sig. |