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 323
6
Diseases
8
Unique genes
0.185
Avg. similarity score
Pendred syndrome
Most-connected disease (5 links)
Disease
Searched: Usher syndrome type 1
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Usher syndrome type 1
Pendred syndrome
Sensorineural hearing loss thrombocytopenia syndrome
progressive microcephaly-seizures-cortical blindness-developmental delay syndrome
Arthrogryposis with ectodermal dysplasia
hearing loss, autosomal recessive 116
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Pendred syndrome | 5 | 5 | 7 |
| Sensorineural hearing loss thrombocytopenia syndrome | 2 | 2 | 1 |
| progressive microcephaly-seizures-cortical blindness-developmental delay syndrome | 2 | 2 | 1 |
| Arthrogryposis with ectodermal dysplasia | 1 | 1 | 1 |
| Usher syndrome type 1 | 1 | 1 | 2 |
| hearing loss, autosomal recessive 116 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| DIAPH1 | 3 / 6 | Pendred syndrome, progressive microcephaly-seizures-cortical blindness-developmental delay syndrome, Sensorineural hearing loss thrombocytopenia syndrome |
| CLDN9 | 2 / 6 | hearing loss, autosomal recessive 116, Pendred syndrome |
| MYO7A | 2 / 6 | Pendred syndrome, Usher syndrome type 1 |
| OTOF | 2 / 6 | Arthrogryposis with ectodermal dysplasia, Pendred 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 ⇵ |
|---|---|---|---|---|---|
| Defective SLC26A4 causes Pendred syndrome (PDS) | Reactome | 1 / 1 | 1,501× | 6.66e-4 | 9.83e-3 ✓ sig. |
| Potassium transport channels | Reactome | 1 / 3 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| Multifunctional anion exchangers | Reactome | 1 / 9 | 167× | 5.98e-3 | 4.93e-2 ✓ sig. |
| ERBB2 Regulates Cell Motility | Reactome | 1 / 15 | 100× | 9.95e-3 | 6.89e-2 |
| Insertion of tail-anchored proteins into the endoplasmic reticulum membrane | Reactome | 1 / 16 | 93.8× | 1.06e-2 | 7.20e-2 |
| The canonical retinoid cycle in rods (twilight vision) | Reactome | 1 / 20 | 75.1× | 1.32e-2 | 8.23e-2 |
| Activation of G protein gated Potassium channels | Reactome | 1 / 29 | 51.8× | 1.92e-2 | 1.03e-1 |
| Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits | Reactome | 1 / 29 | 51.8× | 1.92e-2 | 1.03e-1 |
| Virion - Hepatitis viruses | KEGG | 1 / 48 | 31.3× | 3.15e-2 | 1.36e-1 |
| Thyroid hormone synthesis | KEGG | 1 / 75 | 20.0× | 4.89e-2 | 1.73e-1 |
| Gastric acid secretion | KEGG | 1 / 76 | 19.8× | 4.95e-2 | 1.75e-1 |
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 1 / 101 | 14.9× | 6.53e-2 | 2.02e-1 |
| Leukocyte transendothelial migration | KEGG | 1 / 116 | 12.9× | 7.47e-2 | 2.16e-1 |
| RHO GTPases Activate Formins | Reactome | 1 / 140 | 10.7× | 8.96e-2 | 2.37e-1 |
| Hepatitis C | KEGG | 1 / 159 | 9.4× | 1.01e-1 | 2.55e-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 ⇵ |
|---|---|---|---|---|---|
| sensory perception of sound | GO:0007605 | 5 / 162 | 72.1× | 2.52e-9 | 5.03e-7 ✓ sig. |
| inner ear morphogenesis | GO:0042472 | 3 / 65 | 108× | 2.22e-6 | 1.58e-4 ✓ sig. |
| equilibrioception | GO:0050957 | 2 / 6 | 779× | 2.40e-6 | 1.68e-4 ✓ sig. |
| sensory perception of light stimulus | GO:0050953 | 2 / 13 | 359× | 1.25e-5 | 6.24e-4 ✓ sig. |
| inner ear auditory receptor cell differentiation | GO:0042491 | 2 / 19 | 246× | 2.73e-5 | 1.14e-3 ✓ sig. |
| inner ear receptor cell stereocilium organization | GO:0060122 | 2 / 25 | 187× | 4.79e-5 | 1.75e-3 ✓ sig. |
| sensory organ morphogenesis | GO:0090596 | 1 / 1 | 2,336× | 4.28e-4 | 8.64e-3 ✓ sig. |
| glutamate reuptake | GO:0051935 | 1 / 2 | 1,168× | 8.56e-4 | 1.38e-2 ✓ sig. |
| pigment granule localization | GO:0051875 | 1 / 2 | 1,168× | 8.56e-4 | 1.38e-2 ✓ sig. |
| pigment granule transport | GO:0051904 | 1 / 2 | 1,168× | 8.56e-4 | 1.38e-2 ✓ sig. |
| protein localization to microvillus | GO:1904106 | 1 / 2 | 1,168× | 8.56e-4 | 1.38e-2 ✓ sig. |
| parallel actin filament bundle assembly | GO:0030046 | 1 / 3 | 779× | 1.28e-3 | 1.76e-2 ✓ sig. |
| mechanoreceptor differentiation | GO:0042490 | 1 / 5 | 467× | 2.14e-3 | 2.37e-2 ✓ sig. |
| phagolysosome assembly | GO:0001845 | 1 / 5 | 467× | 2.14e-3 | 2.37e-2 ✓ sig. |
| auditory receptor cell morphogenesis | GO:0002093 | 1 / 6 | 389× | 2.57e-3 | 2.64e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| progressive microcephaly-seizures-cortical blindness-developmental delay syndrome | Sensorineural hearing loss thrombocytopenia syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Arthrogryposis with ectodermal dysplasia | Pendred syndrome | 0.125 | 1 | 4.55e-4 | 9.72e-4 ✓ sig. |
| hearing loss, autosomal recessive 116 | Pendred syndrome | 0.125 | 1 | 4.55e-4 | 9.72e-4 ✓ sig. |
| Pendred syndrome | Sensorineural hearing loss thrombocytopenia syndrome | 0.125 | 1 | 4.55e-4 | 9.72e-4 ✓ sig. |
| Pendred syndrome | progressive microcephaly-seizures-cortical blindness-developmental delay syndrome | 0.125 | 1 | 4.55e-4 | 9.72e-4 ✓ sig. |
| Pendred syndrome | Usher syndrome type 1 | 0.111 | 1 | 9.09e-4 | 1.58e-3 ✓ sig. |