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 417
5
Diseases
5
Unique genes
0.278
Avg. similarity score
Combined deficiency of vitamin k-dependent clotting factors
Most-connected disease (4 links)
Disease
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Combined deficiency of vitamin k-dependent clotting factors
Body skin hyperlaxity
Coumarin resistance
vitamin K-dependent clotting factors, combined deficiency of, type 1
vitamin K-dependent clotting factors, combined deficiency of, type 2
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Combined deficiency of vitamin k-dependent clotting factors | 4 | 4 | 3 |
| Body skin hyperlaxity | 2 | 2 | 1 |
| Coumarin resistance | 2 | 2 | 3 |
| vitamin K-dependent clotting factors, combined deficiency of, type 1 | 2 | 2 | 1 |
| vitamin K-dependent clotting factors, combined deficiency of, type 2 | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GGCX | 3 / 5 | Body skin hyperlaxity, Combined deficiency of vitamin k-dependent clotting factors, vitamin K-dependent clotting factors, combined deficiency of, type 1 |
| VKORC1 | 3 / 5 | Combined deficiency of vitamin k-dependent clotting factors, Coumarin resistance, vitamin K-dependent clotting factors, combined deficiency of, type 2 |
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 ⇵ |
|---|---|---|---|---|---|
| CYP2E1 reactions | Reactome | 2 / 11 | 437× | 7.62e-6 | 2.67e-4 ✓ sig. |
| Ubiquinone and other terpenoid-quinone biosynthesis | KEGG | 2 / 12 | 400× | 9.14e-6 | 3.12e-4 ✓ sig. |
| Biosynthesis of cofactors | KEGG | 3 / 154 | 46.8× | 2.03e-5 | 6.04e-4 ✓ sig. |
| Metabolic pathways | KEGG | 5 / 1,563 | 7.7× | 3.71e-5 | 9.98e-4 ✓ sig. |
| Xenobiotics | Reactome | 2 / 24 | 200× | 3.81e-5 | 1.02e-3 ✓ sig. |
| Retinol metabolism | KEGG | 2 / 68 | 70.6× | 3.12e-4 | 5.54e-3 ✓ sig. |
| Chemical carcinogenesis - DNA adducts | KEGG | 2 / 70 | 68.6× | 3.31e-4 | 5.79e-3 ✓ sig. |
| Drug metabolism - cytochrome P450 | KEGG | 2 / 73 | 65.8× | 3.60e-4 | 6.18e-3 ✓ sig. |
| Metabolism of xenobiotics by cytochrome P450 | KEGG | 2 / 79 | 60.8× | 4.22e-4 | 6.97e-3 ✓ sig. |
| Metabolism of vitamin K | Reactome | 1 / 3 | 801× | 1.25e-3 | 1.60e-2 ✓ sig. |
| Caffeine metabolism | KEGG | 1 / 6 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Biosynthesis of maresin-like SPMs | Reactome | 1 / 6 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Lipid and atherosclerosis | KEGG | 2 / 216 | 22.2× | 3.11e-3 | 3.15e-2 ✓ sig. |
| Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) | Reactome | 1 / 8 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) | Reactome | 1 / 9 | 267× | 3.74e-3 | 3.59e-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 ⇵ |
|---|---|---|---|---|---|
| vitamin K metabolic process | GO:0042373 | 2 / 7 | 1,068× | 1.20e-6 | 9.61e-5 ✓ sig. |
| xenobiotic metabolic process | GO:0006805 | 3 / 120 | 93.4× | 2.56e-6 | 1.75e-4 ✓ sig. |
| epoxygenase P450 pathway | GO:0019373 | 2 / 18 | 415× | 8.75e-6 | 4.70e-4 ✓ sig. |
| xenobiotic catabolic process | GO:0042178 | 2 / 28 | 267× | 2.16e-5 | 9.54e-4 ✓ sig. |
| coumarin catabolic process | GO:0046226 | 1 / 1 | 3,737× | 2.68e-4 | 6.20e-3 ✓ sig. |
| urea metabolic process | GO:0019627 | 1 / 1 | 3,737× | 2.68e-4 | 6.20e-3 ✓ sig. |
| blood coagulation | GO:0007596 | 2 / 106 | 70.5× | 3.15e-4 | 6.96e-3 ✓ sig. |
| steroid metabolic process | GO:0008202 | 2 / 135 | 55.4× | 5.11e-4 | 9.70e-3 ✓ sig. |
| organofluorine metabolic process | GO:0090346 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| peptidyl-glutamic acid carboxylation | GO:0017187 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| negative regulation of bone development | GO:1903011 | 1 / 2 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| negative regulation of testosterone biosynthetic process | GO:2000225 | 1 / 3 | 1,246× | 8.03e-4 | 1.30e-2 ✓ sig. |
| terpenoid metabolic process | GO:0006721 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| S-adenosylmethionine biosynthetic process | GO:0006556 | 1 / 4 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| monoterpenoid metabolic process | GO:0016098 | 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 ⇵ |
|---|---|---|---|---|---|
| Body skin hyperlaxity | vitamin K-dependent clotting factors, combined deficiency of, type 1 | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Body skin hyperlaxity | Combined deficiency of vitamin k-dependent clotting factors | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Combined deficiency of vitamin k-dependent clotting factors | vitamin K-dependent clotting factors, combined deficiency of, type 2 | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Combined deficiency of vitamin k-dependent clotting factors | vitamin K-dependent clotting factors, combined deficiency of, type 1 | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Coumarin resistance | vitamin K-dependent clotting factors, combined deficiency of, type 2 | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Combined deficiency of vitamin k-dependent clotting factors | Coumarin resistance | 0.167 | 1 | 5.84e-4 | 1.14e-3 ✓ sig. |