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 295
6
Diseases
7
Unique genes
0.125
Avg. similarity score
Achromatopsia
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Achromatopsia
ATF6-related retinopathy
CNGA3-related retinopathy
CNGB3-related retinopathy
GNAT2-related retinopathy
PDE6C-related retinopathy
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Achromatopsia | 5 | 5 | 7 |
| ATF6-related retinopathy | 1 | 1 | 1 |
| CNGA3-related retinopathy | 1 | 1 | 1 |
| CNGB3-related retinopathy | 1 | 1 | 1 |
| GNAT2-related retinopathy | 1 | 1 | 1 |
| PDE6C-related retinopathy | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| ATF6 | 2 / 6 | Achromatopsia, ATF6-related retinopathy |
| CNGA3 | 2 / 6 | Achromatopsia, CNGA3-related retinopathy |
| CNGB3 | 2 / 6 | Achromatopsia, CNGB3-related retinopathy |
| GNAT2 | 2 / 6 | Achromatopsia, GNAT2-related retinopathy |
| PDE6C | 2 / 6 | Achromatopsia, PDE6C-related retinopathy |
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 ⇵ |
|---|---|---|---|---|---|
| Purine metabolism | KEGG | 2 / 128 | 26.8× | 2.29e-3 | 2.52e-2 ✓ sig. |
| ATF6 (ATF6-alpha) activates chaperones | Reactome | 1 / 4 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| ATF6 (ATF6-alpha) activates chaperone genes | Reactome | 1 / 9 | 191× | 5.24e-3 | 4.50e-2 ✓ sig. |
| cAMP signaling pathway | KEGG | 2 / 226 | 15.2× | 6.96e-3 | 5.45e-2 |
| PLC beta mediated events | Reactome | 1 / 12 | 143× | 6.97e-3 | 5.45e-2 |
| G-protein activation | Reactome | 1 / 28 | 61.3× | 1.62e-2 | 9.12e-2 |
| Phototransduction | KEGG | 1 / 29 | 59.2× | 1.68e-2 | 9.34e-2 |
| Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding | Reactome | 1 / 42 | 40.9× | 2.42e-2 | 1.15e-1 |
| Ca2+ pathway | Reactome | 1 / 56 | 30.6× | 3.22e-2 | 1.34e-1 |
| Protein processing in endoplasmic reticulum | KEGG | 1 / 171 | 10.0× | 9.55e-2 | 2.42e-1 |
| Lipid and atherosclerosis | KEGG | 1 / 216 | 7.9× | 1.19e-1 | 2.72e-1 |
| G alpha (i) signalling events | Reactome | 1 / 249 | 6.9× | 1.36e-1 | 2.93e-1 |
| Parkinson disease | KEGG | 1 / 268 | 6.4× | 1.46e-1 | 3.05e-1 |
| Amyotrophic lateral sclerosis | KEGG | 1 / 368 | 4.7× | 1.96e-1 | 3.60e-1 |
| Alzheimer disease | KEGG | 1 / 388 | 4.4× | 2.05e-1 | 3.69e-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 ⇵ |
|---|---|---|---|---|---|
| visual perception | GO:0007601 | 6 / 215 | 74.5× | 1.50e-11 | 5.29e-9 ✓ sig. |
| retinal cone cell development | GO:0046549 | 2 / 11 | 485× | 6.60e-6 | 3.74e-4 ✓ sig. |
| signal transduction | GO:0007165 | 6 / 2,125 | 7.5× | 1.36e-5 | 6.62e-4 ✓ sig. |
| monoatomic cation transmembrane transport | GO:0098655 | 2 / 61 | 87.5× | 2.18e-4 | 5.35e-3 ✓ sig. |
| monoatomic cation transport | GO:0006812 | 2 / 61 | 87.5× | 2.18e-4 | 5.35e-3 ✓ sig. |
| positive regulation of ATF6-mediated unfolded protein response | GO:1903893 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| inorganic cation import across plasma membrane | GO:0098659 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| background adaptation | GO:0120302 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| cell migration involved in heart development | GO:0060973 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| regulation of ATF6-mediated unfolded protein response | GO:1903891 | 1 / 3 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| homeostasis of number of retina cells | GO:0048877 | 1 / 3 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| neural tissue regeneration | GO:0097719 | 1 / 3 | 890× | 1.12e-3 | 1.62e-2 ✓ sig. |
| retinal cone cell differentiation | GO:0042670 | 1 / 4 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| cone retinal bipolar cell differentiation | GO:1904390 | 1 / 4 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| detection of light stimulus | GO:0009583 | 1 / 5 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Achromatopsia | ATF6-related retinopathy | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Achromatopsia | CNGA3-related retinopathy | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Achromatopsia | CNGB3-related retinopathy | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Achromatopsia | GNAT2-related retinopathy | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Achromatopsia | PDE6C-related retinopathy | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |