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 287
6
Diseases
34
Unique genes
0.286
Avg. similarity score
Strabismus
Most-connected disease (5 links)
Disease
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Strabismus
19p13.3 microduplication syndrome
Malan overgrowth syndrome
Malan syndrome
marshall-smith syndrome
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 ⇵ |
|---|---|---|---|
| Strabismus | 5 | 5 | 34 |
| 19p13.3 microduplication syndrome | 4 | 4 | 1 |
| Malan overgrowth syndrome | 4 | 4 | 1 |
| Malan syndrome | 4 | 4 | 1 |
| marshall-smith syndrome | 4 | 4 | 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 |
|---|---|---|
| NFIX | 5 / 6 | 19p13.3 microduplication syndrome, Malan overgrowth syndrome, Malan syndrome, marshall-smith syndrome and 1 more |
| DHX30 | 2 / 6 | neurodevelopmental disorder with severe motor impairment and absent language, 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 | 2 / 16 | 44.2× | 9.11e-4 | 1.27e-2 ✓ sig. |
| Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) | Reactome | 1 / 1 | 353× | 2.83e-3 | 2.95e-2 ✓ sig. |
| Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) | Reactome | 1 / 1 | 353× | 2.83e-3 | 2.95e-2 ✓ sig. |
| GPVI-mediated activation cascade | Reactome | 2 / 34 | 20.8× | 4.12e-3 | 3.86e-2 ✓ sig. |
| Lactose synthesis | Reactome | 1 / 3 | 118× | 8.47e-3 | 6.20e-2 |
| Melanin biosynthesis | Reactome | 1 / 5 | 70.6× | 1.41e-2 | 8.38e-2 |
| MET activates PTPN11 | Reactome | 1 / 5 | 70.6× | 1.41e-2 | 8.38e-2 |
| Adipocytokine signaling pathway | KEGG | 2 / 70 | 10.1× | 1.67e-2 | 9.29e-2 |
| Renal cell carcinoma | KEGG | 2 / 70 | 10.1× | 1.67e-2 | 9.29e-2 |
| RAS signaling downstream of NF1 loss-of-function variants | Reactome | 1 / 7 | 50.5× | 1.97e-2 | 1.02e-1 |
| Synaptic vesicle cycle | KEGG | 2 / 79 | 8.9× | 2.09e-2 | 1.05e-1 |
| Vitamin C (ascorbate) metabolism | Reactome | 1 / 8 | 44.2× | 2.24e-2 | 1.10e-1 |
| Platelet Aggregation (Plug Formation) | Reactome | 1 / 8 | 44.2× | 2.24e-2 | 1.10e-1 |
| Sodium/Proton exchangers | Reactome | 1 / 9 | 39.2× | 2.52e-2 | 1.17e-1 |
| Activation of the phototransduction cascade | Reactome | 1 / 9 | 39.2× | 2.52e-2 | 1.17e-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 ⇵ |
|---|---|---|---|---|---|
| brain development | GO:0007420 | 5 / 244 | 11.3× | 7.44e-5 | 2.43e-3 ✓ sig. |
| dendrite extension | GO:0097484 | 2 / 10 | 110× | 1.43e-4 | 3.96e-3 ✓ sig. |
| histone mRNA catabolic process | GO:0071044 | 2 / 14 | 78.5× | 2.88e-4 | 6.53e-3 ✓ sig. |
| cerebral cortex development | GO:0021987 | 3 / 88 | 18.7× | 5.43e-4 | 1.01e-2 ✓ sig. |
| nuclear-transcribed mRNA catabolic process | GO:0000956 | 2 / 24 | 45.8× | 8.65e-4 | 1.37e-2 ✓ sig. |
| Rac protein signal transduction | GO:0016601 | 2 / 26 | 42.3× | 1.02e-3 | 1.52e-2 ✓ sig. |
| positive regulation of signal transduction | GO:0009967 | 2 / 29 | 37.9× | 1.26e-3 | 1.75e-2 ✓ sig. |
| neurotransmitter secretion | GO:0007269 | 2 / 29 | 37.9× | 1.26e-3 | 1.75e-2 ✓ sig. |
| regulation of macrophage colony-stimulating factor production | GO:1901256 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
| positive regulation of mast cell apoptotic process | GO:0033027 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
| regulation of glial cell differentiation | GO:0045685 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
| observational learning | GO:0098597 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
| beta-catenin-TCF complex assembly | GO:1904837 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
| protein heterotrimerization | GO:0070208 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
| negative regulation of cortisol secretion | GO:0051463 | 1 / 1 | 550× | 1.82e-3 | 2.15e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| 19p13.3 microduplication syndrome | Malan syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| 19p13.3 microduplication syndrome | marshall-smith syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| 19p13.3 microduplication syndrome | Malan overgrowth syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Malan overgrowth syndrome | Malan syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Malan overgrowth syndrome | marshall-smith syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Malan syndrome | marshall-smith syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| 19p13.3 microduplication syndrome | Strabismus | 0.029 | 1 | 2.21e-3 | 3.10e-3 ✓ sig. |
| Malan overgrowth syndrome | Strabismus | 0.029 | 1 | 2.21e-3 | 3.10e-3 ✓ sig. |
| Malan syndrome | Strabismus | 0.029 | 1 | 2.21e-3 | 3.10e-3 ✓ sig. |
| marshall-smith syndrome | Strabismus | 0.029 | 1 | 2.21e-3 | 3.10e-3 ✓ sig. |
| neurodevelopmental disorder with severe motor impairment and absent language | Strabismus | 0.029 | 1 | 2.21e-3 | 3.10e-3 ✓ sig. |