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 265
7
Diseases
18
Unique genes
0.186
Avg. similarity score
Cataract-glaucoma syndrome
Most-connected disease (5 links)
Disease
Searched: cataract 50 with or without glaucoma
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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cataract 50 with or without glaucoma
Cataract-glaucoma syndrome
Mulibrey nanism
Birk-barel syndrome
Stomach disease
Congenital cataract anterior segment dysgenesis syndrome
Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cataract-glaucoma syndrome | 5 | 5 | 2 |
| Mulibrey nanism | 5 | 5 | 4 |
| Birk-barel syndrome | 4 | 4 | 2 |
| Stomach disease | 4 | 4 | 12 |
| cataract 50 with or without glaucoma | 4 | 4 | 1 |
| Congenital cataract anterior segment dysgenesis syndrome | 1 | 1 | 1 |
| Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TRPM3 | 5 / 7 | Birk-barel syndrome, cataract 50 with or without glaucoma, Cataract-glaucoma syndrome, Mulibrey nanism and 1 more |
| PITX3 | 2 / 7 | Cataract-glaucoma syndrome, Congenital cataract anterior segment dysgenesis syndrome |
| PNPLA7 | 2 / 7 | Mulibrey nanism, Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development |
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 ⇵ |
|---|---|---|---|---|---|
| Type I diabetes mellitus | KEGG | 2 / 44 | 30.3× | 1.93e-3 | 2.27e-2 ✓ sig. |
| SDK interactions | Reactome | 1 / 2 | 334× | 3.00e-3 | 3.11e-2 ✓ sig. |
| TWIK-releated acid-sensitive K+ channel (TASK) | Reactome | 1 / 2 | 334× | 3.00e-3 | 3.11e-2 ✓ sig. |
| MECP2 regulates neuronal receptors and channels | Reactome | 1 / 4 | 167× | 5.98e-3 | 5.03e-2 |
| Formyl peptide receptors bind formyl peptides and many other ligands | Reactome | 1 / 8 | 83.4× | 1.19e-2 | 7.79e-2 |
| Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) | Reactome | 1 / 14 | 47.7× | 2.08e-2 | 1.08e-1 |
| G alpha (q) signalling events | Reactome | 2 / 172 | 7.8× | 2.68e-2 | 1.25e-1 |
| Toll Like Receptor 4 (TLR4) Cascade | Reactome | 1 / 19 | 35.1× | 2.81e-2 | 1.28e-1 |
| Phase 4 - resting membrane potential | Reactome | 1 / 19 | 35.1× | 2.81e-2 | 1.28e-1 |
| Synthesis, secretion, and deacylation of Ghrelin | Reactome | 1 / 19 | 35.1× | 2.81e-2 | 1.28e-1 |
| Translocation of ZAP-70 to Immunological synapse | Reactome | 1 / 19 | 35.1× | 2.81e-2 | 1.28e-1 |
| Interleukin-37 signaling | Reactome | 1 / 21 | 31.8× | 3.10e-2 | 1.35e-1 |
| Phosphorylation of CD3 and TCR zeta chains | Reactome | 1 / 22 | 30.3× | 3.25e-2 | 1.38e-1 |
| PD-1 signaling | Reactome | 1 / 23 | 29.0× | 3.39e-2 | 1.42e-1 |
| Glucagon signaling in metabolic regulation | Reactome | 1 / 26 | 25.7× | 3.83e-2 | 1.51e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of interleukin-1 production | GO:0032652 | 1 / 1 | 1,038× | 9.63e-4 | 1.50e-2 ✓ sig. |
| negative regulation of aldosterone secretion | GO:2000859 | 1 / 1 | 1,038× | 9.63e-4 | 1.50e-2 ✓ sig. |
| negative regulation of gliogenesis | GO:0014014 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| response to methamphetamine hydrochloride | GO:1904313 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| positive regulation of cell proliferation in midbrain | GO:1904935 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| cellular response to glial cell derived neurotrophic factor | GO:1990792 | 1 / 2 | 519× | 1.93e-3 | 2.26e-2 ✓ sig. |
| protein dephosphorylation | GO:0006470 | 2 / 72 | 28.8× | 2.15e-3 | 2.41e-2 ✓ sig. |
| regulation of action potential firing rate | GO:0099605 | 1 / 3 | 346× | 2.89e-3 | 2.82e-2 ✓ sig. |
| myoblast migration involved in skeletal muscle regeneration | GO:0014839 | 1 / 4 | 260× | 3.85e-3 | 3.28e-2 ✓ sig. |
| regulation of hormone secretion | GO:0046883 | 1 / 4 | 260× | 3.85e-3 | 3.28e-2 ✓ sig. |
| regulation of leukocyte migration | GO:0002685 | 1 / 5 | 208× | 4.81e-3 | 3.65e-2 ✓ sig. |
| positive regulation of neutrophil apoptotic process | GO:0033031 | 1 / 5 | 208× | 4.81e-3 | 3.65e-2 ✓ sig. |
| negative regulation of T-helper 2 cell differentiation | GO:0045629 | 1 / 5 | 208× | 4.81e-3 | 3.65e-2 ✓ sig. |
| granulocyte chemotaxis | GO:0071621 | 1 / 5 | 208× | 4.81e-3 | 3.65e-2 ✓ sig. |
| positive regulation of T-helper 1 cell differentiation | GO:0045627 | 1 / 6 | 173× | 5.77e-3 | 3.99e-2 ✓ sig. |