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 360
5
Diseases
35
Unique genes
0.028
Avg. similarity score
Ovarian cysts
Most-connected disease (4 links)
Disease
Searched: Ovarian cysts
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Ovarian cysts
Bosch-boonstra-schaaf optic atrophy syndrome
Cataract-growth hormone deficiency-skeletal dysplasia syndrome
amyotrophic lateral sclerosis type 9
immunodeficiency, common variable, 5
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Ovarian cysts | 4 | 4 | 35 |
| Bosch-boonstra-schaaf optic atrophy syndrome | 1 | 1 | 1 |
| Cataract-growth hormone deficiency-skeletal dysplasia syndrome | 1 | 1 | 1 |
| amyotrophic lateral sclerosis type 9 | 1 | 1 | 1 |
| immunodeficiency, common variable, 5 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ANG | 2 / 5 | amyotrophic lateral sclerosis type 9, Ovarian cysts |
| IARS2 | 2 / 5 | Cataract-growth hormone deficiency-skeletal dysplasia syndrome, Ovarian cysts |
| MS4A1 | 2 / 5 | immunodeficiency, common variable, 5, Ovarian cysts |
| NR2F1 | 2 / 5 | Bosch-boonstra-schaaf optic atrophy syndrome, Ovarian cysts |
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 CYP17A1 causes Adrenal hyperplasia 5 (AH5) | Reactome | 1 / 1 | 343× | 2.91e-3 | 3.06e-2 ✓ sig. |
| COX reactions | Reactome | 1 / 1 | 343× | 2.91e-3 | 3.06e-2 ✓ sig. |
| Adherens junctions interactions | Reactome | 2 / 32 | 21.4× | 3.87e-3 | 3.74e-2 ✓ sig. |
| Coronavirus disease - COVID-19 | KEGG | 4 / 238 | 5.8× | 4.86e-3 | 4.37e-2 ✓ sig. |
| Defective Mismatch Repair Associated With MSH6 | Reactome | 1 / 2 | 172× | 5.82e-3 | 4.95e-2 ✓ sig. |
| Defective Mismatch Repair Associated With MSH3 | Reactome | 1 / 2 | 172× | 5.82e-3 | 4.95e-2 ✓ sig. |
| Defective Mismatch Repair Associated With MSH2 | Reactome | 1 / 3 | 114× | 8.72e-3 | 6.44e-2 |
| Efferocytosis | KEGG | 3 / 157 | 6.6× | 1.06e-2 | 7.26e-2 |
| HHAT G278V abrogates palmitoylation of Hh-Np | Reactome | 1 / 4 | 85.8× | 1.16e-2 | 7.66e-2 |
| Alternative complement activation | Reactome | 1 / 5 | 68.6× | 1.45e-2 | 8.76e-2 |
| CLEC7A/inflammasome pathway | Reactome | 1 / 6 | 57.2× | 1.74e-2 | 9.78e-2 |
| Classical antibody-mediated complement activation | Reactome | 1 / 6 | 57.2× | 1.74e-2 | 9.78e-2 |
| Prolactin signaling pathway | KEGG | 2 / 71 | 9.7× | 1.81e-2 | 1.00e-1 |
| Epithelial cell signaling in Helicobacter pylori infection | KEGG | 2 / 71 | 9.7× | 1.81e-2 | 1.00e-1 |
| IkBA variant leads to EDA-ID | Reactome | 1 / 7 | 49.0× | 2.02e-2 | 1.06e-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 ⇵ |
|---|---|---|---|---|---|
| proteoglycan metabolic process | GO:0006029 | 2 / 11 | 97.1× | 1.85e-4 | 4.89e-3 ✓ sig. |
| positive regulation of canonical Wnt signaling pathway | GO:0090263 | 3 / 115 | 13.9× | 1.29e-3 | 1.79e-2 ✓ sig. |
| vitelline membrane formation | GO:0030704 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| negative regulation of eye pigmentation | GO:0048074 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| camera-type eye photoreceptor cell fate commitment | GO:0060220 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| peroxisome transport along microtubule | GO:0036250 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| positive regulation of neurotransmitter uptake | GO:0051582 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| negative regulation of spontaneous neurotransmitter secretion | GO:1904049 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| negative regulation of eosinophil extravasation | GO:2000420 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| negative regulation of sodium-dependent phosphate transport | GO:2000119 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| regulation of systemic arterial blood pressure by circulatory renin-angiotensin | GO:0001991 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| positive regulation of tyrosinase activity | GO:0032773 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| negative regulation of timing of catagen | GO:0051796 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| positive regulation of melanosome transport | GO:1902910 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
| cytoskeletal rearrangement involved in phagocytosis, engulfment | GO:0060097 | 1 / 1 | 534× | 1.87e-3 | 2.24e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| amyotrophic lateral sclerosis type 9 | Ovarian cysts | 0.028 | 1 | 2.27e-3 | 3.19e-3 ✓ sig. |
| Bosch-boonstra-schaaf optic atrophy syndrome | Ovarian cysts | 0.028 | 1 | 2.27e-3 | 3.19e-3 ✓ sig. |
| Cataract-growth hormone deficiency-skeletal dysplasia syndrome | Ovarian cysts | 0.028 | 1 | 2.27e-3 | 3.19e-3 ✓ sig. |
| immunodeficiency, common variable, 5 | Ovarian cysts | 0.028 | 1 | 2.27e-3 | 3.19e-3 ✓ sig. |