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 399
5
Diseases
12
Unique genes
0.175
Avg. similarity score
Coenzyme q10 deficiency
Most-connected disease (4 links)
Disease
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Coenzyme q10 deficiency
Primary coenzyme q10 deficiency
Coq7-related distal hereditary motor neuropathy
primary coenzyme Q10 deficiency 8
Deafness, encephaloneuropathy, obesity, valvulopathy syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Coenzyme q10 deficiency | 4 | 4 | 12 |
| Primary coenzyme q10 deficiency | 3 | 3 | 2 |
| Coq7-related distal hereditary motor neuropathy | 2 | 2 | 1 |
| primary coenzyme Q10 deficiency 8 | 2 | 2 | 1 |
| Deafness, encephaloneuropathy, obesity, valvulopathy syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| COQ6 | 3 / 5 | Coenzyme q10 deficiency, Primary coenzyme q10 deficiency, primary coenzyme Q10 deficiency 8 |
| COQ7 | 3 / 5 | Coenzyme q10 deficiency, Coq7-related distal hereditary motor neuropathy, Primary coenzyme q10 deficiency |
| PDSS1 | 2 / 5 | Coenzyme q10 deficiency, Deafness, encephaloneuropathy, obesity, valvulopathy 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 ⇵ |
|---|---|---|---|---|---|
| Ubiquinone and other terpenoid-quinone biosynthesis | KEGG | 5 / 12 | 417× | 3.00e-13 | 7.06e-11 ✓ sig. |
| Biosynthesis of cofactors | KEGG | 5 / 154 | 32.5× | 2.39e-7 | 1.40e-5 ✓ sig. |
| Ubiquinol biosynthesis | Reactome | 2 / 3 | 667× | 2.74e-6 | 1.15e-4 ✓ sig. |
| Terpenoid backbone biosynthesis | KEGG | 2 / 23 | 87.0× | 2.29e-4 | 4.35e-3 ✓ sig. |
| Metabolic pathways | KEGG | 6 / 1,563 | 3.8× | 2.21e-3 | 2.45e-2 ✓ sig. |
| Phosphate bond hydrolysis by NTPDase proteins | Reactome | 1 / 8 | 125× | 7.97e-3 | 5.96e-2 |
| Purinergic signaling in leishmaniasis infection | Reactome | 1 / 24 | 41.7× | 2.37e-2 | 1.13e-1 |
| RHO GTPases Activate WASPs and WAVEs | Reactome | 1 / 36 | 27.8× | 3.54e-2 | 1.42e-1 |
| Base excision repair | KEGG | 1 / 44 | 22.7× | 4.31e-2 | 1.58e-1 |
| Pyrimidine metabolism | KEGG | 1 / 58 | 17.3× | 5.65e-2 | 1.83e-1 |
| FCGR3A-mediated phagocytosis | Reactome | 1 / 59 | 17.0× | 5.74e-2 | 1.84e-1 |
| Regulation of actin dynamics for phagocytic cup formation | Reactome | 1 / 60 | 16.7× | 5.84e-2 | 1.86e-1 |
| VEGFA-VEGFR2 Pathway | Reactome | 1 / 62 | 16.1× | 6.02e-2 | 1.89e-1 |
| Nucleotide metabolism | KEGG | 1 / 85 | 11.8× | 8.17e-2 | 2.22e-1 |
| Purine metabolism | KEGG | 1 / 128 | 7.8× | 1.21e-1 | 2.74e-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 ⇵ |
|---|---|---|---|---|---|
| ubiquinone biosynthetic process | GO:0006744 | 9 / 17 | 824× | 6.99e-27 | 2.72e-23 ✓ sig. |
| isoprenoid biosynthetic process | GO:0008299 | 3 / 13 | 359× | 5.77e-8 | 7.64e-6 ✓ sig. |
| UDP-alpha-D-glucose metabolic process | GO:0006011 | 1 / 3 | 519× | 1.93e-3 | 2.20e-2 ✓ sig. |
| UDP catabolic process | GO:0006256 | 1 / 3 | 519× | 1.93e-3 | 2.20e-2 ✓ sig. |
| 'de novo' post-translational protein folding | GO:0051084 | 1 / 4 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
| cell projection morphogenesis | GO:0048858 | 1 / 6 | 260× | 3.85e-3 | 3.22e-2 ✓ sig. |
| regulation of body fluid levels | GO:0050878 | 1 / 7 | 222× | 4.49e-3 | 3.47e-2 ✓ sig. |
| lamellipodium morphogenesis | GO:0072673 | 1 / 7 | 222× | 4.49e-3 | 3.47e-2 ✓ sig. |
| positive regulation of protein tyrosine kinase activity | GO:0061098 | 1 / 9 | 173× | 5.77e-3 | 3.94e-2 ✓ sig. |
| single strand break repair | GO:0000012 | 1 / 12 | 130× | 7.68e-3 | 4.52e-2 ✓ sig. |
| glycerol metabolic process | GO:0006071 | 1 / 12 | 130× | 7.68e-3 | 4.52e-2 ✓ sig. |
| phosphorylation | GO:0016310 | 1 / 14 | 111× | 8.96e-3 | 4.84e-2 ✓ sig. |
| megakaryocyte development | GO:0035855 | 1 / 23 | 67.7× | 1.47e-2 | 6.16e-2 |
| actin polymerization or depolymerization | GO:0008154 | 1 / 23 | 67.7× | 1.47e-2 | 6.16e-2 |
| regulation of reactive oxygen species metabolic process | GO:2000377 | 1 / 27 | 57.7× | 1.72e-2 | 6.67e-2 |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Coenzyme q10 deficiency | Primary coenzyme q10 deficiency | 0.154 | 2 | 5.57e-7 | 3.60e-6 ✓ sig. |
| Coq7-related distal hereditary motor neuropathy | Primary coenzyme q10 deficiency | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Primary coenzyme q10 deficiency | primary coenzyme Q10 deficiency 8 | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Coenzyme q10 deficiency | primary coenzyme Q10 deficiency 8 | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Coenzyme q10 deficiency | Deafness, encephaloneuropathy, obesity, valvulopathy syndrome | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |
| Coenzyme q10 deficiency | Coq7-related distal hereditary motor neuropathy | 0.077 | 1 | 7.79e-4 | 1.39e-3 ✓ sig. |