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 495
6
Diseases
5
Unique genes
0.315
Avg. similarity score
Corneal opacity
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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Corneal opacity
Gm1 gangliosidosis
Mucopolysaccharidosis type 4B
Mucopolysaccharidosis type ivb (morquio)
White matter abnormality
Proximal renal tubular acidosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Corneal opacity | 5 | 5 | 4 |
| Gm1 gangliosidosis | 4 | 4 | 2 |
| Mucopolysaccharidosis type 4B | 4 | 4 | 1 |
| Mucopolysaccharidosis type ivb (morquio) | 4 | 4 | 1 |
| White matter abnormality | 4 | 4 | 1 |
| Proximal renal tubular acidosis | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GLB1 | 5 / 6 | Corneal opacity, Gm1 gangliosidosis, Mucopolysaccharidosis type 4B, Mucopolysaccharidosis type ivb (morquio) and 1 more |
| SLC4A4 | 2 / 6 | Corneal opacity, Proximal renal tubular acidosis |
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 ⇵ |
|---|---|---|---|---|---|
| MPS IV - Morquio syndrome B | Reactome | 1 / 1 | 2,402× | 4.16e-4 | 5.79e-3 ✓ sig. |
| Defective SLC4A4 causes renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) | Reactome | 1 / 1 | 2,402× | 4.16e-4 | 5.79e-3 ✓ sig. |
| Defective NEU1 causes sialidosis | Reactome | 1 / 3 | 801× | 1.25e-3 | 1.34e-2 ✓ sig. |
| Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant | Reactome | 1 / 7 | 343× | 2.91e-3 | 2.49e-2 ✓ sig. |
| Bicarbonate transporters | Reactome | 1 / 10 | 240× | 4.16e-3 | 3.21e-2 ✓ sig. |
| Keratan sulfate degradation | Reactome | 1 / 13 | 185× | 5.40e-3 | 3.84e-2 ✓ sig. |
| RUNX3 regulates NOTCH signaling | Reactome | 1 / 14 | 172× | 5.82e-3 | 4.03e-2 ✓ sig. |
| Glycosphingolipid biosynthesis - ganglio series | KEGG | 1 / 15 | 160× | 6.23e-3 | 4.21e-2 ✓ sig. |
| Constitutive Signaling by NOTCH1 HD Domain Mutants | Reactome | 1 / 15 | 160× | 6.23e-3 | 4.21e-2 ✓ sig. |
| Other glycan degradation | KEGG | 1 / 18 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| Glycosaminoglycan degradation | KEGG | 1 / 19 | 126× | 7.89e-3 | 4.92e-2 ✓ sig. |
| NOTCH3 Activation and Transmission of Signal to the Nucleus | Reactome | 1 / 19 | 126× | 7.89e-3 | 4.92e-2 ✓ sig. |
| HS-GAG degradation | Reactome | 1 / 22 | 109× | 9.13e-3 | 5.37e-2 |
| Proximal tubule bicarbonate reclamation | KEGG | 1 / 23 | 104× | 9.54e-3 | 5.53e-2 |
| Galactose metabolism | KEGG | 1 / 32 | 75.1× | 1.33e-2 | 6.74e-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 ⇵ |
|---|---|---|---|---|---|
| endocardial cushion cell development | GO:0061444 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| response to cortisone | GO:0051413 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| keratan sulfate proteoglycan catabolic process | GO:0042340 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| response to Thyroglobulin triiodothyronine | GO:1904016 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| distal tubule development | GO:0072017 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| loop of Henle development | GO:0072070 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| ciliary body morphogenesis | GO:0061073 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| cardiac neural crest cell development involved in outflow tract morphogenesis | GO:0061309 | 1 / 4 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| galactose catabolic process | GO:0019388 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| inhibition of neuroepithelial cell differentiation | GO:0002085 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| positive regulation of myeloid cell differentiation | GO:0045639 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| positive regulation of cardiac epithelial to mesenchymal transition | GO:0062043 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
| pulmonary artery morphogenesis | GO:0061156 | 1 / 6 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| negative regulation of endothelial cell differentiation | GO:0045602 | 1 / 7 | 534× | 1.87e-3 | 2.05e-2 ✓ sig. |
| ganglioside catabolic process | GO:0006689 | 1 / 8 | 467× | 2.14e-3 | 2.19e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Mucopolysaccharidosis type 4B | White matter abnormality | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Mucopolysaccharidosis type 4B | Mucopolysaccharidosis type ivb (morquio) | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Mucopolysaccharidosis type ivb (morquio) | White matter abnormality | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Gm1 gangliosidosis | Mucopolysaccharidosis type 4B | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Gm1 gangliosidosis | White matter abnormality | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Gm1 gangliosidosis | Mucopolysaccharidosis type ivb (morquio) | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Corneal opacity | Mucopolysaccharidosis type 4B | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Corneal opacity | White matter abnormality | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Corneal opacity | Mucopolysaccharidosis type ivb (morquio) | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Corneal opacity | Proximal renal tubular acidosis | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Corneal opacity | Gm1 gangliosidosis | 0.167 | 1 | 5.16e-4 | 9.13e-4 ✓ sig. |