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 403
5
Diseases
5
Unique genes
0.327
Avg. similarity score
Chuvash erythrocytosis
Most-connected disease (4 links)
Disease
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Chuvash erythrocytosis
Erythrocytosis due to tissue hypoxemia
Pancreatic cyst
Von hippel-lindau syndrome
von hippel-lindau disease
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Chuvash erythrocytosis | 4 | 4 | 1 |
| Erythrocytosis due to tissue hypoxemia | 4 | 4 | 1 |
| Pancreatic cyst | 4 | 4 | 2 |
| Von hippel-lindau syndrome | 4 | 4 | 4 |
| von hippel-lindau disease | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| VHL | 5 / 5 | Chuvash erythrocytosis, Erythrocytosis due to tissue hypoxemia, Pancreatic cyst, von hippel-lindau disease 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 ⇵ |
|---|---|---|---|---|---|
| Prostate cancer | KEGG | 2 / 98 | 49.0× | 6.49e-4 | 9.77e-3 ✓ sig. |
| Interleukin-4 and Interleukin-13 signaling | Reactome | 2 / 108 | 44.5× | 7.87e-4 | 1.14e-2 ✓ sig. |
| PTK6 Regulates Cell Cycle | Reactome | 1 / 6 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| RUNX3 regulates WNT signaling | Reactome | 1 / 8 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| EGFR Transactivation by Gastrin | Reactome | 1 / 9 | 267× | 3.74e-3 | 3.59e-2 ✓ sig. |
| RUNX3 regulates p14-ARF | Reactome | 1 / 9 | 267× | 3.74e-3 | 3.59e-2 ✓ sig. |
| Transcriptional regulation by RUNX2 | Reactome | 1 / 12 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Regulation of RUNX1 Expression and Activity | Reactome | 1 / 16 | 150× | 6.64e-3 | 5.28e-2 |
| VxPx cargo-targeting to cilium | Reactome | 1 / 21 | 114× | 8.71e-3 | 6.31e-2 |
| Citric acid cycle (TCA cycle) | Reactome | 1 / 22 | 109× | 9.13e-3 | 6.50e-2 |
| Estrogen-dependent nuclear events downstream of ESR-membrane signaling | Reactome | 1 / 23 | 104× | 9.54e-3 | 6.67e-2 |
| Citrate cycle (TCA cycle) | KEGG | 1 / 30 | 80.1× | 1.24e-2 | 7.78e-2 |
| Activation of Matrix Metalloproteinases | Reactome | 1 / 33 | 72.8× | 1.37e-2 | 8.23e-2 |
| Thyroid cancer | KEGG | 1 / 37 | 64.9× | 1.53e-2 | 8.81e-2 |
| Transcriptional Regulation by VENTX | Reactome | 1 / 38 | 63.2× | 1.57e-2 | 8.96e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of G1/S transition of mitotic cell cycle | GO:2000045 | 2 / 57 | 131× | 9.09e-5 | 2.82e-3 ✓ sig. |
| liver development | GO:0001889 | 2 / 87 | 85.9× | 2.12e-4 | 5.27e-3 ✓ sig. |
| metanephric distal tubule morphogenesis | GO:0072287 | 1 / 1 | 3,737× | 2.68e-4 | 6.20e-3 ✓ sig. |
| nitrogen cycle metabolic process | GO:0071941 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| lymph vessel morphogenesis | GO:0036303 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| metanephric proximal tubule development | GO:0072237 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| response to UV-A | GO:0070141 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| re-entry into mitotic cell cycle | GO:0000320 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| calcium-independent cell-matrix adhesion | GO:0007161 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| metanephric ascending thin limb development | GO:0072218 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| succinate metabolic process | GO:0006105 | 1 / 5 | 747× | 1.34e-3 | 1.79e-2 ✓ sig. |
| mitochondrial electron transport, succinate to ubiquinone | GO:0006121 | 1 / 5 | 747× | 1.34e-3 | 1.79e-2 ✓ sig. |
| Wnt signaling pathway | GO:0016055 | 2 / 232 | 32.2× | 1.50e-3 | 1.91e-2 ✓ sig. |
| response to vitamin E | GO:0033197 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| mesonephric duct development | GO:0072177 | 1 / 6 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Chuvash erythrocytosis | Erythrocytosis due to tissue hypoxemia | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Chuvash erythrocytosis | von hippel-lindau disease | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Erythrocytosis due to tissue hypoxemia | von hippel-lindau disease | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Chuvash erythrocytosis | Pancreatic cyst | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Erythrocytosis due to tissue hypoxemia | Pancreatic cyst | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Pancreatic cyst | von hippel-lindau disease | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Chuvash erythrocytosis | Von hippel-lindau syndrome | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Erythrocytosis due to tissue hypoxemia | Von hippel-lindau syndrome | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| von hippel-lindau disease | Von hippel-lindau syndrome | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Pancreatic cyst | Von hippel-lindau syndrome | 0.167 | 1 | 5.19e-4 | 1.04e-3 ✓ sig. |