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 231
7
Diseases
20
Unique genes
0.177
Avg. similarity score
Apraxia
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Apraxia
Cataplexy
Niemann-Pick disease, type C1
Niemann-pick disease
Ophthalmoplegia
Marinesco-sjogren syndrome
Niemann-Pick disease, type C2
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Apraxia | 4 | 4 | 10 |
| Cataplexy | 4 | 4 | 1 |
| Niemann-Pick disease, type C1 | 4 | 4 | 1 |
| Niemann-pick disease | 4 | 4 | 8 |
| Ophthalmoplegia | 4 | 4 | 2 |
| Marinesco-sjogren syndrome | 1 | 1 | 3 |
| Niemann-Pick disease, type C2 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NPC1 | 5 / 7 | Apraxia, Cataplexy, Niemann-pick disease, Niemann-Pick disease, type C1 and 1 more |
| NPC2 | 2 / 7 | Niemann-pick disease, Niemann-Pick disease, type C2 |
| SIL1 | 2 / 7 | Apraxia, Marinesco-sjogren syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| LDL clearance | Reactome | 3 / 18 | 100× | 3.17e-6 | 1.30e-4 ✓ sig. |
| Lysosome | KEGG | 4 / 133 | 18.1× | 6.07e-5 | 1.49e-3 ✓ sig. |
| Cholesterol metabolism | KEGG | 3 / 51 | 35.3× | 7.82e-5 | 1.83e-3 ✓ sig. |
| Virion - Ebolavirus, Lyssavirus and Morbillivirus | KEGG | 1 / 12 | 50.0× | 1.98e-2 | 1.02e-1 |
| Steroid biosynthesis | KEGG | 1 / 20 | 30.0× | 3.28e-2 | 1.36e-1 |
| Adherens junctions interactions | Reactome | 1 / 32 | 18.8× | 5.20e-2 | 1.75e-1 |
| Glycosphingolipid metabolism | Reactome | 1 / 46 | 13.1× | 7.39e-2 | 2.11e-1 |
| Pyruvate metabolism | KEGG | 1 / 47 | 12.8× | 7.55e-2 | 2.13e-1 |
| Synthesis of PIPs at the plasma membrane | Reactome | 1 / 51 | 11.8× | 8.17e-2 | 2.22e-1 |
| Sphingolipid metabolism | KEGG | 1 / 54 | 11.1× | 8.63e-2 | 2.29e-1 |
| Hedgehog signaling pathway | KEGG | 1 / 56 | 10.7× | 8.93e-2 | 2.33e-1 |
| Hedgehog 'off' state | Reactome | 1 / 56 | 10.7× | 8.93e-2 | 2.33e-1 |
| Degradation of GLI1 by the proteasome | Reactome | 1 / 57 | 10.5× | 9.08e-2 | 2.35e-1 |
| GLI3 is processed to GLI3R by the proteasome | Reactome | 1 / 60 | 10.0× | 9.54e-2 | 2.41e-1 |
| Basal cell carcinoma | KEGG | 1 / 63 | 9.5× | 9.99e-2 | 2.48e-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 ⇵ |
|---|---|---|---|---|---|
| cholesterol storage | GO:0010878 | 3 / 5 | 561× | 1.05e-8 | 1.78e-6 ✓ sig. |
| cholesterol efflux | GO:0033344 | 4 / 31 | 121× | 2.95e-8 | 4.32e-6 ✓ sig. |
| sterol metabolic process | GO:0016125 | 3 / 22 | 127× | 1.59e-6 | 1.20e-4 ✓ sig. |
| cholesterol transport | GO:0030301 | 3 / 28 | 100× | 3.38e-6 | 2.20e-4 ✓ sig. |
| cholesterol metabolic process | GO:0008203 | 4 / 107 | 34.9× | 4.59e-6 | 2.80e-4 ✓ sig. |
| intracellular cholesterol transport | GO:0032367 | 2 / 13 | 144× | 8.43e-5 | 2.66e-3 ✓ sig. |
| liver development | GO:0001889 | 3 / 87 | 32.2× | 1.05e-4 | 3.13e-3 ✓ sig. |
| sterol transport | GO:0015918 | 2 / 17 | 110× | 1.47e-4 | 4.02e-3 ✓ sig. |
| gene expression | GO:0010467 | 4 / 269 | 13.9× | 1.70e-4 | 4.49e-3 ✓ sig. |
| spleen development | GO:0048536 | 2 / 42 | 44.5× | 9.13e-4 | 1.42e-2 ✓ sig. |
| programmed cell death | GO:0012501 | 2 / 42 | 44.5× | 9.13e-4 | 1.42e-2 ✓ sig. |
| negative regulation of neuron remodeling | GO:1904800 | 1 / 1 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| negative regulation of branching morphogenesis of a nerve | GO:2000173 | 1 / 1 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| caudate nucleus development | GO:0021757 | 1 / 1 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| putamen development | GO:0021758 | 1 / 1 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Cataplexy | Niemann-Pick disease, type C1 | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Cataplexy | Ophthalmoplegia | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Niemann-Pick disease, type C1 | Ophthalmoplegia | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Cataplexy | Niemann-pick disease | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Niemann-pick disease | Niemann-Pick disease, type C1 | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Niemann-pick disease | Niemann-Pick disease, type C2 | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Apraxia | Cataplexy | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Apraxia | Niemann-Pick disease, type C1 | 0.091 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Niemann-pick disease | Ophthalmoplegia | 0.100 | 1 | 1.04e-3 | 1.72e-3 ✓ sig. |
| Apraxia | Ophthalmoplegia | 0.083 | 1 | 1.30e-3 | 2.04e-3 ✓ sig. |
| Apraxia | Marinesco-sjogren syndrome | 0.077 | 1 | 1.95e-3 | 2.81e-3 ✓ sig. |