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 281
6
Diseases
56
Unique genes
0.094
Avg. similarity score
Amblyopia
Most-connected disease (4 links)
Disease
Searched: CNGB1-related retinopathy
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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CNGB1-related retinopathy
Amblyopia
Strabismus
Christianson syndrome
Neurodegenerative disorder, x-linked, female-restricted, with parkinsonism and cognitive impairment
neurodevelopmental disorder with severe motor impairment and absent language
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Amblyopia | 4 | 4 | 25 |
| Strabismus | 4 | 4 | 34 |
| Christianson syndrome | 3 | 3 | 1 |
| Neurodegenerative disorder, x-linked, female-restricted, with parkinsonism and cognitive impairment | 3 | 3 | 1 |
| CNGB1-related retinopathy | 1 | 1 | 1 |
| neurodevelopmental disorder with severe motor impairment and absent language | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SLC9A6 | 4 / 6 | Amblyopia, Christianson syndrome, Neurodegenerative disorder, x-linked, female-restricted, with parkinsonism and cognitive impairment, Strabismus |
| CNGB1 | 2 / 6 | Amblyopia, CNGB1-related retinopathy |
| DHX30 | 2 / 6 | neurodevelopmental disorder with severe motor impairment and absent language, Strabismus |
| GALC | 2 / 6 | Amblyopia, Strabismus |
| KMT2D | 2 / 6 | Amblyopia, Strabismus |
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 ⇵ |
|---|---|---|---|---|---|
| Regulation of insulin secretion | Reactome | 3 / 16 | 40.2× | 5.15e-5 | 1.37e-3 ✓ sig. |
| Melanin biosynthesis | Reactome | 2 / 5 | 85.8× | 2.12e-4 | 4.18e-3 ✓ sig. |
| Activation of the phototransduction cascade | Reactome | 2 / 9 | 47.7× | 7.53e-4 | 1.13e-2 ✓ sig. |
| Presynaptic depolarization and calcium channel opening | Reactome | 2 / 12 | 35.7× | 1.37e-3 | 1.79e-2 ✓ sig. |
| Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon | Reactome | 2 / 18 | 23.8× | 3.11e-3 | 3.24e-2 ✓ sig. |
| Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) | Reactome | 1 / 1 | 214× | 4.66e-3 | 4.32e-2 ✓ sig. |
| Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) | Reactome | 1 / 1 | 214× | 4.66e-3 | 4.32e-2 ✓ sig. |
| PD-1 signaling | Reactome | 2 / 23 | 18.6× | 5.07e-3 | 4.57e-2 ✓ sig. |
| Phototransduction | KEGG | 2 / 29 | 14.8× | 8.00e-3 | 6.14e-2 |
| GABAergic synapse | KEGG | 3 / 89 | 7.2× | 8.22e-3 | 6.26e-2 |
| GPVI-mediated activation cascade | Reactome | 2 / 34 | 12.6× | 1.09e-2 | 7.49e-2 |
| Molecules associated with elastic fibres | Reactome | 2 / 38 | 11.3× | 1.35e-2 | 8.47e-2 |
| Lactose synthesis | Reactome | 1 / 3 | 71.5× | 1.39e-2 | 8.64e-2 |
| Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors | Reactome | 1 / 3 | 71.5× | 1.39e-2 | 8.64e-2 |
| Cholinergic synapse | KEGG | 3 / 115 | 5.6× | 1.64e-2 | 9.54e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| negative regulation of osteoclast differentiation | GO:0045671 | 4 / 30 | 44.5× | 1.87e-6 | 1.41e-4 ✓ sig. |
| melanin biosynthetic process from tyrosine | GO:0006583 | 2 / 4 | 167× | 5.27e-5 | 1.94e-3 ✓ sig. |
| calcium ion import across plasma membrane | GO:0098703 | 3 / 28 | 35.8× | 7.92e-5 | 2.64e-3 ✓ sig. |
| calcium ion transmembrane transport | GO:0070588 | 5 / 149 | 11.2× | 8.30e-5 | 2.74e-3 ✓ sig. |
| axon extension | GO:0048675 | 3 / 37 | 27.1× | 1.84e-4 | 4.93e-3 ✓ sig. |
| pigmentation | GO:0043473 | 3 / 39 | 25.7× | 2.16e-4 | 5.50e-3 ✓ sig. |
| positive regulation of bone mineralization | GO:0030501 | 3 / 42 | 23.8× | 2.69e-4 | 6.43e-3 ✓ sig. |
| photoreceptor cell maintenance | GO:0045494 | 3 / 45 | 22.2× | 3.31e-4 | 7.41e-3 ✓ sig. |
| adult feeding behavior | GO:0008343 | 2 / 10 | 66.7× | 3.91e-4 | 8.34e-3 ✓ sig. |
| dendrite extension | GO:0097484 | 2 / 10 | 66.7× | 3.91e-4 | 8.34e-3 ✓ sig. |
| osteoclast differentiation | GO:0030316 | 3 / 49 | 20.4× | 4.26e-4 | 8.87e-3 ✓ sig. |
| visual perception | GO:0007601 | 5 / 215 | 7.8× | 4.56e-4 | 9.31e-3 ✓ sig. |
| melanin biosynthetic process | GO:0042438 | 2 / 14 | 47.7× | 7.84e-4 | 1.34e-2 ✓ sig. |
| regulation of tumor necrosis factor production | GO:0032680 | 2 / 14 | 47.7× | 7.84e-4 | 1.34e-2 ✓ sig. |
| histone mRNA catabolic process | GO:0071044 | 2 / 14 | 47.7× | 7.84e-4 | 1.34e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Amblyopia | Strabismus | 0.053 | 3 | 2.19e-5 | 1.03e-4 ✓ sig. |
| Christianson syndrome | Neurodegenerative disorder, x-linked, female-restricted, with parkinsonism and cognitive impairment | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Amblyopia | Christianson syndrome | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Amblyopia | CNGB1-related retinopathy | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Amblyopia | Neurodegenerative disorder, x-linked, female-restricted, with parkinsonism and cognitive impairment | 0.038 | 1 | 1.62e-3 | 2.46e-3 ✓ sig. |
| Christianson syndrome | Strabismus | 0.029 | 1 | 2.21e-3 | 3.11e-3 ✓ sig. |
| Neurodegenerative disorder, x-linked, female-restricted, with parkinsonism and cognitive impairment | Strabismus | 0.029 | 1 | 2.21e-3 | 3.11e-3 ✓ sig. |
| neurodevelopmental disorder with severe motor impairment and absent language | Strabismus | 0.029 | 1 | 2.21e-3 | 3.11e-3 ✓ sig. |