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 429
5
Diseases
2
Unique genes
0.405
Avg. similarity score
Dihydrolipoamide dehydrogenase deficiency
Most-connected disease (4 links)
Disease
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Dihydrolipoamide dehydrogenase deficiency
Congenital methemoglobinemia
Cytochrome-b5 reductase deficiency
methemoglobinemia due to deficiency of methemoglobin reductase
pyruvate dehydrogenase E3 deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Dihydrolipoamide dehydrogenase deficiency | 4 | 4 | 2 |
| Congenital methemoglobinemia | 3 | 3 | 1 |
| Cytochrome-b5 reductase deficiency | 3 | 3 | 1 |
| methemoglobinemia due to deficiency of methemoglobin reductase | 3 | 3 | 1 |
| pyruvate dehydrogenase E3 deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CYB5R3 | 4 / 5 | Congenital methemoglobinemia, Cytochrome-b5 reductase deficiency, Dihydrolipoamide dehydrogenase deficiency, methemoglobinemia due to deficiency of methemoglobin reductase |
| DLD | 2 / 5 | Dihydrolipoamide dehydrogenase deficiency, pyruvate dehydrogenase E3 deficiency |
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 ⇵ |
|---|---|---|---|---|---|
| Glycine degradation | Reactome | 1 / 4 | 1,501× | 6.66e-4 | 9.96e-3 ✓ sig. |
| Vitamin C (ascorbate) metabolism | Reactome | 1 / 8 | 751× | 1.33e-3 | 1.68e-2 ✓ sig. |
| Lysine catabolism | Reactome | 1 / 12 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| Biosynthesis of various nucleotide sugars | KEGG | 1 / 15 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Regulation of pyruvate dehydrogenase (PDH) complex | Reactome | 1 / 16 | 375× | 2.66e-3 | 2.83e-2 ✓ sig. |
| Lipoic acid metabolism | KEGG | 1 / 19 | 316× | 3.16e-3 | 3.20e-2 ✓ sig. |
| Pyruvate metabolism | Reactome | 1 / 19 | 316× | 3.16e-3 | 3.20e-2 ✓ sig. |
| Branched-chain amino acid catabolism | Reactome | 1 / 20 | 300× | 3.33e-3 | 3.31e-2 ✓ sig. |
| Phase I - Functionalization of compounds | Reactome | 1 / 21 | 286× | 3.49e-3 | 3.42e-2 ✓ sig. |
| Signaling by Retinoic Acid | Reactome | 1 / 21 | 286× | 3.49e-3 | 3.42e-2 ✓ sig. |
| Citric acid cycle (TCA cycle) | Reactome | 1 / 22 | 273× | 3.66e-3 | 3.54e-2 ✓ sig. |
| Glyoxylate metabolism and glycine degradation | Reactome | 1 / 28 | 214× | 4.66e-3 | 4.18e-2 ✓ sig. |
| Citrate cycle (TCA cycle) | KEGG | 1 / 30 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Glyoxylate and dicarboxylate metabolism | KEGG | 1 / 30 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Propanoate metabolism | KEGG | 1 / 32 | 188× | 5.32e-3 | 4.56e-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 ⇵ |
|---|---|---|---|---|---|
| 2-oxoglutarate decarboxylation to succinyl-CoA | GO:0120551 | 1 / 1 | 9,344× | 1.07e-4 | 3.18e-3 ✓ sig. |
| pyruvate metabolic process | GO:0006090 | 1 / 4 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA | GO:0120552 | 1 / 4 | 2,336× | 4.28e-4 | 8.59e-3 ✓ sig. |
| pyruvate decarboxylation to acetyl-CoA | GO:0006086 | 1 / 7 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| branched-chain amino acid catabolic process | GO:0009083 | 1 / 18 | 519× | 1.93e-3 | 2.20e-2 ✓ sig. |
| 2-oxoglutarate metabolic process | GO:0006103 | 1 / 18 | 519× | 1.93e-3 | 2.20e-2 ✓ sig. |
| nitric oxide biosynthetic process | GO:0006809 | 1 / 23 | 406× | 2.46e-3 | 2.53e-2 ✓ sig. |
| sperm capacitation | GO:0048240 | 1 / 25 | 374× | 2.67e-3 | 2.65e-2 ✓ sig. |
| sterol biosynthetic process | GO:0016126 | 1 / 31 | 301× | 3.32e-3 | 2.98e-2 ✓ sig. |
| gastrulation | GO:0007369 | 1 / 38 | 246× | 4.06e-3 | 3.30e-2 ✓ sig. |
| cholesterol biosynthetic process | GO:0006695 | 1 / 39 | 240× | 4.17e-3 | 3.34e-2 ✓ sig. |
| blood circulation | GO:0008015 | 1 / 41 | 228× | 4.38e-3 | 3.43e-2 ✓ sig. |
| mitochondrial electron transport, NADH to ubiquinone | GO:0006120 | 1 / 47 | 199× | 5.02e-3 | 3.69e-2 ✓ sig. |
| steroid biosynthetic process | GO:0006694 | 1 / 65 | 144× | 6.94e-3 | 4.33e-2 ✓ sig. |
| regulation of membrane potential | GO:0042391 | 1 / 85 | 110× | 9.08e-3 | 4.88e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Congenital methemoglobinemia | Cytochrome-b5 reductase deficiency | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital methemoglobinemia | methemoglobinemia due to deficiency of methemoglobin reductase | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Cytochrome-b5 reductase deficiency | methemoglobinemia due to deficiency of methemoglobin reductase | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Congenital methemoglobinemia | Dihydrolipoamide dehydrogenase deficiency | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Cytochrome-b5 reductase deficiency | Dihydrolipoamide dehydrogenase deficiency | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Dihydrolipoamide dehydrogenase deficiency | pyruvate dehydrogenase E3 deficiency | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Dihydrolipoamide dehydrogenase deficiency | methemoglobinemia due to deficiency of methemoglobin reductase | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |