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 357
6
Diseases
48
Unique genes
0.105
Avg. similarity score
Multiple epiphyseal dysplasia with early-onset diabetes mellitus
Most-connected disease (3 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Multiple epiphyseal dysplasia with early-onset diabetes mellitus
Progressive supranuclear palsy
Sialolithiasis
Wolcott-rallison syndrome
IL21-related infantile inflammatory bowel disease
TRAF3 haploinsufficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Multiple epiphyseal dysplasia with early-onset diabetes mellitus | 3 | 3 | 1 |
| Progressive supranuclear palsy | 3 | 3 | 27 |
| Sialolithiasis | 3 | 3 | 22 |
| Wolcott-rallison syndrome | 3 | 3 | 1 |
| IL21-related infantile inflammatory bowel disease | 1 | 1 | 1 |
| TRAF3 haploinsufficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| EIF2AK3 | 4 / 6 | Multiple epiphyseal dysplasia with early-onset diabetes mellitus, Progressive supranuclear palsy, Sialolithiasis, Wolcott-rallison syndrome |
| IL21 | 2 / 6 | IL21-related infantile inflammatory bowel disease, Progressive supranuclear palsy |
| TRAF3 | 2 / 6 | Sialolithiasis, TRAF3 haploinsufficiency |
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 HK1 causes hexokinase deficiency (HK deficiency) | Reactome | 1 / 1 | 250× | 4.00e-3 | 3.77e-2 ✓ sig. |
| Acetylation | Reactome | 1 / 2 | 125× | 7.98e-3 | 5.96e-2 |
| Inositol transporters | Reactome | 1 / 2 | 125× | 7.98e-3 | 5.96e-2 |
| Mitophagy - animal | KEGG | 3 / 105 | 7.1× | 8.44e-3 | 6.19e-2 |
| Th17 cell differentiation | KEGG | 3 / 109 | 6.9× | 9.35e-3 | 6.59e-2 |
| TRAF3 deficiency - HSE | Reactome | 1 / 3 | 83.4× | 1.19e-2 | 7.61e-2 |
| RUNX2 regulates osteoblast differentiation | Reactome | 1 / 3 | 83.4× | 1.19e-2 | 7.61e-2 |
| RUNX2 regulates genes involved in differentiation of myeloid cells | Reactome | 1 / 4 | 62.6× | 1.59e-2 | 9.02e-2 |
| Yersinia infection | KEGG | 3 / 138 | 5.4× | 1.76e-2 | 9.60e-2 |
| Measles | KEGG | 3 / 139 | 5.4× | 1.80e-2 | 9.71e-2 |
| Alcoholic liver disease | KEGG | 3 / 144 | 5.2× | 1.97e-2 | 1.02e-1 |
| Neomycin, kanamycin and gentamicin biosynthesis | KEGG | 1 / 5 | 50.0× | 1.98e-2 | 1.02e-1 |
| PERK regulates gene expression | Reactome | 1 / 5 | 50.0× | 1.98e-2 | 1.02e-1 |
| RUNX2 regulates genes involved in cell migration | Reactome | 1 / 5 | 50.0× | 1.98e-2 | 1.02e-1 |
| Caffeine metabolism | KEGG | 1 / 6 | 41.7× | 2.37e-2 | 1.13e-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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of mitochondrial fission | GO:0090258 | 2 / 5 | 156× | 6.43e-5 | 2.17e-3 ✓ sig. |
| positive regulation of tissue remodeling | GO:0034105 | 2 / 6 | 130× | 9.63e-5 | 2.94e-3 ✓ sig. |
| positive regulation of amyloid-beta formation | GO:1902004 | 2 / 21 | 37.1× | 1.32e-3 | 1.78e-2 ✓ sig. |
| chondrocyte development | GO:0002063 | 2 / 21 | 37.1× | 1.32e-3 | 1.78e-2 ✓ sig. |
| regulation of JNK cascade | GO:0046328 | 2 / 23 | 33.9× | 1.58e-3 | 1.98e-2 ✓ sig. |
| positive regulation of interleukin-17 production | GO:0032740 | 2 / 27 | 28.8× | 2.18e-3 | 2.37e-2 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 6 / 532 | 4.4× | 2.30e-3 | 2.45e-2 ✓ sig. |
| cell-cell adhesion | GO:0098609 | 4 / 218 | 7.1× | 2.35e-3 | 2.48e-2 ✓ sig. |
| amyloid fibril formation | GO:1990000 | 2 / 29 | 26.8× | 2.51e-3 | 2.57e-2 ✓ sig. |
| plus-end-directed organelle transport along microtubule | GO:0072386 | 1 / 1 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| positive regulation of neurotransmitter uptake | GO:0051582 | 1 / 1 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| negative regulation of spontaneous neurotransmitter secretion | GO:1904049 | 1 / 1 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| ligamentous ossification | GO:0036076 | 1 / 1 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| positive regulation of cell fate determination | GO:1905935 | 1 / 1 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| mitochondrial tryptophanyl-tRNA aminoacylation | GO:0070183 | 1 / 1 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Multiple epiphyseal dysplasia with early-onset diabetes mellitus | Wolcott-rallison syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Multiple epiphyseal dysplasia with early-onset diabetes mellitus | Sialolithiasis | 0.043 | 1 | 1.43e-3 | 2.21e-3 ✓ sig. |
| Sialolithiasis | TRAF3 haploinsufficiency | 0.043 | 1 | 1.43e-3 | 2.21e-3 ✓ sig. |
| Sialolithiasis | Wolcott-rallison syndrome | 0.043 | 1 | 1.43e-3 | 2.21e-3 ✓ sig. |
| IL21-related infantile inflammatory bowel disease | Progressive supranuclear palsy | 0.036 | 1 | 1.75e-3 | 2.59e-3 ✓ sig. |
| Multiple epiphyseal dysplasia with early-onset diabetes mellitus | Progressive supranuclear palsy | 0.036 | 1 | 1.75e-3 | 2.59e-3 ✓ sig. |
| Progressive supranuclear palsy | Wolcott-rallison syndrome | 0.036 | 1 | 1.75e-3 | 2.59e-3 ✓ sig. |