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 567
5
Diseases
8
Unique genes
0.306
Avg. similarity score
Café-au-lait macules
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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Café-au-lait macules
Increased nuchal translucency
Schwannomatosis-2, susceptibility to
Congenital malformation syndromes associated with short stature
Schwannomatosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Café-au-lait macules | 4 | 4 | 1 |
| Increased nuchal translucency | 4 | 4 | 1 |
| Schwannomatosis-2, susceptibility to | 4 | 4 | 1 |
| Congenital malformation syndromes associated with short stature | 3 | 3 | 6 |
| Schwannomatosis | 3 | 3 | 3 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LZTR1 | 5 / 5 | Café-au-lait macules, Congenital malformation syndromes associated with short stature, Increased nuchal translucency, Schwannomatosis and 1 more |
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 ⇵ |
|---|---|---|---|---|---|
| Renal cell carcinoma | KEGG | 3 / 70 | 64.3× | 1.04e-5 | 3.01e-4 ✓ sig. |
| Chronic myeloid leukemia | KEGG | 3 / 77 | 58.5× | 1.39e-5 | 3.82e-4 ✓ sig. |
| Spry regulation of FGF signaling | Reactome | 2 / 16 | 188× | 4.64e-5 | 1.03e-3 ✓ sig. |
| Neurotrophin signaling pathway | KEGG | 3 / 120 | 37.5× | 5.25e-5 | 1.13e-3 ✓ sig. |
| Natural killer cell mediated cytotoxicity | KEGG | 3 / 133 | 33.9× | 7.14e-5 | 1.45e-3 ✓ sig. |
| Hepatocellular carcinoma | KEGG | 3 / 170 | 26.5× | 1.48e-4 | 2.59e-3 ✓ sig. |
| Proteoglycans in cancer | KEGG | 3 / 204 | 22.1× | 2.54e-4 | 3.96e-3 ✓ sig. |
| Chemical carcinogenesis - reactive oxygen species | KEGG | 3 / 227 | 19.8× | 3.48e-4 | 5.05e-3 ✓ sig. |
| Endometrial cancer | KEGG | 2 / 59 | 50.9× | 6.52e-4 | 8.20e-3 ✓ sig. |
| Acute myeloid leukemia | KEGG | 2 / 68 | 44.2× | 8.65e-4 | 1.02e-2 ✓ sig. |
| Non-small cell lung cancer | KEGG | 2 / 73 | 41.1× | 9.97e-4 | 1.13e-2 ✓ sig. |
| Glioma | KEGG | 2 / 76 | 39.5× | 1.08e-3 | 1.20e-2 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 2 / 80 | 37.5× | 1.20e-3 | 1.30e-2 ✓ sig. |
| ErbB signaling pathway | KEGG | 2 / 86 | 34.9× | 1.38e-3 | 1.45e-2 ✓ sig. |
| Colorectal cancer | KEGG | 2 / 87 | 34.5× | 1.41e-3 | 1.47e-2 ✓ sig. |
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 | 3 / 244 | 28.7× | 1.17e-4 | 3.47e-3 ✓ sig. |
| positive regulation of stress fiber assembly | GO:0051496 | 2 / 53 | 88.1× | 2.19e-4 | 5.40e-3 ✓ sig. |
| epidermal growth factor receptor signaling pathway | GO:0007173 | 2 / 64 | 73.0× | 3.19e-4 | 7.04e-3 ✓ sig. |
| negative regulation of cortisol secretion | GO:0051463 | 1 / 1 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| negative regulation of growth hormone secretion | GO:0060125 | 1 / 1 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| intestinal epithelial cell migration | GO:0061582 | 1 / 1 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| single stranded viral RNA replication via double stranded DNA intermediate | GO:0039692 | 1 / 1 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| Ras protein signal transduction | GO:0007265 | 2 / 79 | 59.1× | 4.86e-4 | 9.30e-3 ✓ sig. |
| positive regulation of cell differentiation | GO:0045597 | 2 / 83 | 56.3× | 5.36e-4 | 9.90e-3 ✓ sig. |
| microvillus organization | GO:0032528 | 1 / 2 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| regulation of gliogenesis | GO:0014013 | 1 / 2 | 1,168× | 8.56e-4 | 1.33e-2 ✓ sig. |
| positive T cell selection | GO:0043368 | 1 / 3 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| CD4-positive or CD8-positive, alpha-beta T cell lineage commitment | GO:0043369 | 1 / 3 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| Schwann cell proliferation | GO:0014010 | 1 / 3 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| positive regulation of glucose mediated signaling pathway | GO:1902661 | 1 / 3 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Café-au-lait macules | Increased nuchal translucency | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Café-au-lait macules | Schwannomatosis-2, susceptibility to | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Increased nuchal translucency | Schwannomatosis-2, susceptibility to | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Café-au-lait macules | Schwannomatosis | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Increased nuchal translucency | Schwannomatosis | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Schwannomatosis | Schwannomatosis-2, susceptibility to | 0.250 | 1 | 1.94e-4 | 4.41e-4 ✓ sig. |
| Café-au-lait macules | Congenital malformation syndromes associated with short stature | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Congenital malformation syndromes associated with short stature | Increased nuchal translucency | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Congenital malformation syndromes associated with short stature | Schwannomatosis-2, susceptibility to | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |