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 604
5
Diseases
6
Unique genes
0.296
Avg. similarity score
Choroidal melanoma
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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Choroidal melanoma
Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome
Spondylometaepiphyseal dysplasia, short limb-hand type
Warburg-cinotti syndrome
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Choroidal melanoma | 4 | 4 | 6 |
| Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome | 3 | 3 | 1 |
| Spondylometaepiphyseal dysplasia, short limb-hand type | 3 | 3 | 1 |
| Warburg-cinotti syndrome | 3 | 3 | 1 |
| Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| DDR2 | 4 / 5 | Choroidal melanoma, Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome, Spondylometaepiphyseal dysplasia, short limb-hand type, Warburg-cinotti syndrome |
| TDP1 | 2 / 5 | Choroidal melanoma, Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 |
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 ⇵ |
|---|---|---|---|---|---|
| mRNA decay by 5' to 3' exoribonuclease | Reactome | 1 / 14 | 143× | 6.98e-3 | 4.53e-2 ✓ sig. |
| Non-integrin membrane-ECM interactions | Reactome | 1 / 24 | 83.4× | 1.19e-2 | 6.32e-2 |
| Vasopressin regulates renal water homeostasis via Aquaporins | Reactome | 1 / 43 | 46.6× | 2.13e-2 | 8.89e-2 |
| Base excision repair | KEGG | 1 / 44 | 45.5× | 2.18e-2 | 9.00e-2 |
| Nonhomologous End-Joining (NHEJ) | Reactome | 1 / 69 | 29.0× | 3.40e-2 | 1.16e-1 |
| RNA degradation | KEGG | 1 / 78 | 25.7× | 3.83e-2 | 1.24e-1 |
| Spliceosome | KEGG | 1 / 162 | 12.4× | 7.83e-2 | 1.87e-1 |
| mRNA Splicing - Major Pathway | Reactome | 1 / 183 | 10.9× | 8.80e-2 | 2.00e-1 |
| Endocytosis | KEGG | 1 / 250 | 8.0× | 1.19e-1 | 2.40e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of hepatic stellate cell proliferation | GO:1904899 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| TRAM-dependent toll-like receptor 4 signaling pathway | GO:0035669 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| positive regulation of hepatic stellate cell activation | GO:2000491 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| regulation of extracellular matrix disassembly | GO:0010715 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| regulation of tissue remodeling | GO:0034103 | 1 / 6 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
| negative regulation of hydrogen peroxide-mediated programmed cell death | GO:1901299 | 1 / 6 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
| endochondral bone growth | GO:0003416 | 1 / 10 | 311× | 3.21e-3 | 2.69e-2 ✓ sig. |
| positive regulation of extracellular matrix disassembly | GO:0090091 | 1 / 11 | 283× | 3.53e-3 | 2.82e-2 ✓ sig. |
| collagen-activated tyrosine kinase receptor signaling pathway | GO:0038063 | 1 / 12 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |
| single strand break repair | GO:0000012 | 1 / 12 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |
| insulin secretion involved in cellular response to glucose stimulus | GO:0035773 | 1 / 12 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |
| positive regulation of fibroblast migration | GO:0010763 | 1 / 14 | 222× | 4.49e-3 | 3.17e-2 ✓ sig. |
| chondrocyte proliferation | GO:0035988 | 1 / 15 | 208× | 4.81e-3 | 3.27e-2 ✓ sig. |
| P-body assembly | GO:0033962 | 1 / 16 | 195× | 5.13e-3 | 3.37e-2 ✓ sig. |
| cellular response to angiotensin | GO:1904385 | 1 / 16 | 195× | 5.13e-3 | 3.37e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome | Warburg-cinotti syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome | Spondylometaepiphyseal dysplasia, short limb-hand type | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Spondylometaepiphyseal dysplasia, short limb-hand type | Warburg-cinotti syndrome | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Choroidal melanoma | Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Choroidal melanoma | Warburg-cinotti syndrome | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Choroidal melanoma | Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |
| Choroidal melanoma | Spondylometaepiphyseal dysplasia, short limb-hand type | 0.143 | 1 | 3.87e-4 | 7.33e-4 ✓ sig. |