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 217
8
Diseases
5
Unique genes
0.326
Avg. similarity score
Blue cone monochromatism
Most-connected disease (6 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) ·
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Blue cone monochromatism
Cone monochromatism
X-linked cone dysfunction syndrome with myopia
Deuteranomaly
red-green color blindness
Cone dystrophy, x-linked
red color blindness
Tritanopia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Blue cone monochromatism | 6 | 6 | 3 |
| Cone monochromatism | 6 | 6 | 2 |
| X-linked cone dysfunction syndrome with myopia | 6 | 6 | 2 |
| Deuteranomaly | 5 | 5 | 2 |
| red-green color blindness | 5 | 5 | 1 |
| Cone dystrophy, x-linked | 4 | 4 | 2 |
| red color blindness | 3 | 3 | 1 |
| Tritanopia | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| OPN1MW | 6 / 8 | Blue cone monochromatism, Cone dystrophy, x-linked, Cone monochromatism, Deuteranomaly and 2 more |
| OPN1LW | 4 / 8 | Blue cone monochromatism, Cone monochromatism, red color blindness, X-linked cone dysfunction syndrome with myopia |
| OPN1SW | 2 / 8 | Blue cone monochromatism, Tritanopia |
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 ⇵ |
|---|---|---|---|---|---|
| The retinoid cycle in cones (daylight vision) | Reactome | 3 / 8 | 901× | 1.94e-9 | 2.01e-7 ✓ sig. |
| Opsins | Reactome | 3 / 10 | 721× | 4.15e-9 | 4.01e-7 ✓ sig. |
| Retinoid cycle disease events | Reactome | 3 / 13 | 554× | 9.90e-9 | 8.64e-7 ✓ sig. |
| G alpha (i) signalling events | Reactome | 3 / 249 | 28.9× | 8.54e-5 | 1.97e-3 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| absorption of visible light | GO:0016038 | 4 / 6 | 2,492× | 1.48e-14 | 9.32e-12 ✓ sig. |
| detection of visible light | GO:0009584 | 4 / 15 | 997× | 1.34e-12 | 6.04e-10 ✓ sig. |
| cellular response to light stimulus | GO:0071482 | 4 / 16 | 934× | 1.79e-12 | 7.75e-10 ✓ sig. |
| phototransduction | GO:0007602 | 4 / 34 | 440× | 4.56e-11 | 1.42e-8 ✓ sig. |
| visual perception | GO:0007601 | 5 / 215 | 86.9× | 1.92e-10 | 5.16e-8 ✓ sig. |
| positive regulation of cytokinesis | GO:0032467 | 3 / 41 | 273× | 9.77e-8 | 1.18e-5 ✓ sig. |
| G protein-coupled receptor signaling pathway | GO:0007186 | 4 / 1,031 | 14.5× | 4.40e-5 | 1.64e-3 ✓ sig. |
| signal transduction | GO:0007165 | 4 / 2,125 | 7.0× | 7.58e-4 | 1.26e-2 ✓ sig. |
| protein localization to non-motile cilium | GO:0097499 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| cellular response to UV-A | GO:0071492 | 1 / 11 | 340× | 2.94e-3 | 2.79e-2 ✓ sig. |
| eye photoreceptor cell development | GO:0042462 | 1 / 21 | 178× | 5.61e-3 | 3.88e-2 ✓ sig. |
| intraciliary transport | GO:0042073 | 1 / 36 | 104× | 9.60e-3 | 5.01e-2 |
| cilium organization | GO:0044782 | 1 / 40 | 93.4× | 1.07e-2 | 5.29e-2 |
| positive regulation of autophagy | GO:0010508 | 1 / 92 | 40.6× | 2.44e-2 | 7.94e-2 |
| cell projection organization | GO:0030030 | 1 / 214 | 17.5× | 5.60e-2 | 1.23e-1 |