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 404
5
Diseases
7
Unique genes
0.208
Avg. similarity score
Maple syrup urine disease
Most-connected disease (4 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Maple syrup urine disease
Thiamine-responsive maple syrup urine disease
maple syrup urine disease type 1A
maple syrup urine disease type 1B
maple syrup urine disease, mild variant
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Maple syrup urine disease | 4 | 4 | 7 |
| Thiamine-responsive maple syrup urine disease | 3 | 3 | 3 |
| maple syrup urine disease type 1A | 2 | 2 | 1 |
| maple syrup urine disease type 1B | 2 | 2 | 1 |
| maple syrup urine disease, mild variant | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| BCKDHA | 3 / 5 | Maple syrup urine disease, maple syrup urine disease type 1A, Thiamine-responsive maple syrup urine disease |
| BCKDHB | 3 / 5 | Maple syrup urine disease, maple syrup urine disease type 1B, Thiamine-responsive maple syrup urine disease |
| DBT | 2 / 5 | Maple syrup urine disease, Thiamine-responsive maple syrup urine disease |
| PPM1K | 2 / 5 | Maple syrup urine disease, maple syrup urine disease, mild variant |
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 ⇵ |
|---|---|---|---|---|---|
| Branched-chain amino acid catabolism | Reactome | 7 / 20 | 601× | 1.09e-20 | 9.52e-18 ✓ sig. |
| 2-Oxocarboxylic acid metabolism | KEGG | 5 / 33 | 260× | 2.39e-12 | 4.85e-10 ✓ sig. |
| Valine, leucine and isoleucine degradation | KEGG | 5 / 48 | 179× | 1.72e-11 | 2.92e-9 ✓ sig. |
| Lipoic acid metabolism | KEGG | 4 / 19 | 361× | 1.56e-10 | 2.17e-8 ✓ sig. |
| Glyoxylate metabolism and glycine degradation | Reactome | 4 / 28 | 245× | 8.23e-10 | 9.43e-8 ✓ sig. |
| Propanoate metabolism | KEGG | 4 / 32 | 214× | 1.44e-9 | 1.54e-7 ✓ sig. |
| Metabolic pathways | KEGG | 5 / 1,563 | 5.5× | 6.20e-4 | 9.44e-3 ✓ sig. |
| Valine, leucine and isoleucine biosynthesis | KEGG | 1 / 4 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| Glycine degradation | Reactome | 1 / 4 | 429× | 2.33e-3 | 2.55e-2 ✓ sig. |
| Biosynthesis of cofactors | KEGG | 2 / 154 | 22.3× | 3.29e-3 | 3.29e-2 ✓ sig. |
| Lysine catabolism | Reactome | 1 / 12 | 143× | 6.97e-3 | 5.45e-2 |
| Regulation of pyruvate dehydrogenase (PDH) complex | Reactome | 1 / 16 | 107× | 9.29e-3 | 6.56e-2 |
| Pyruvate metabolism | Reactome | 1 / 19 | 90.3× | 1.10e-2 | 7.27e-2 |
| Pantothenate and CoA biosynthesis | KEGG | 1 / 21 | 81.7× | 1.22e-2 | 7.72e-2 |
| Signaling by Retinoic Acid | Reactome | 1 / 21 | 81.7× | 1.22e-2 | 7.72e-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 ⇵ |
|---|---|---|---|---|---|
| branched-chain amino acid catabolic process | GO:0009083 | 7 / 18 | 1,038× | 2.02e-22 | 4.58e-19 ✓ sig. |
| branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA | GO:0120552 | 4 / 4 | 2,670× | 6.89e-15 | 4.58e-12 ✓ sig. |
| L-isoleucine catabolic process | GO:0006550 | 2 / 5 | 1,068× | 1.20e-6 | 9.61e-5 ✓ sig. |
| 2-oxoglutarate decarboxylation to succinyl-CoA | GO:0120551 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| isoleucine metabolic process | GO:0006549 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| L-leucine metabolic process | GO:0006551 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| valine metabolic process | GO:0006573 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| branched-chain amino acid biosynthetic process | GO:0009082 | 1 / 2 | 1,335× | 7.49e-4 | 1.25e-2 ✓ sig. |
| pyruvate metabolic process | GO:0006090 | 1 / 4 | 667× | 1.50e-3 | 1.91e-2 ✓ sig. |
| L-valine catabolic process | GO:0006574 | 1 / 5 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| amino acid catabolic process | GO:0009063 | 1 / 5 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| branched-chain amino acid metabolic process | GO:0009081 | 1 / 5 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| regulation of hormone levels | GO:0010817 | 1 / 5 | 534× | 1.87e-3 | 2.19e-2 ✓ sig. |
| L-leucine catabolic process | GO:0006552 | 1 / 7 | 381× | 2.62e-3 | 2.62e-2 ✓ sig. |
| regulation of pyruvate decarboxylation to acetyl-CoA | GO:0010510 | 1 / 7 | 381× | 2.62e-3 | 2.62e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Maple syrup urine disease | Thiamine-responsive maple syrup urine disease | 0.375 | 3 | 5.75e-11 | 6.20e-10 ✓ sig. |
| maple syrup urine disease type 1A | Thiamine-responsive maple syrup urine disease | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| maple syrup urine disease type 1B | Thiamine-responsive maple syrup urine disease | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Maple syrup urine disease | maple syrup urine disease type 1B | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Maple syrup urine disease | maple syrup urine disease type 1A | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Maple syrup urine disease | maple syrup urine disease, mild variant | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |