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 326
7
Diseases
7
Unique genes
0.383
Avg. similarity score
Homocystinuria with megaloblastic anemia
Most-connected disease (6 links)
Disease
Searched: Inborn disorder of cobalamin metabolism and transport
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Inborn disorder of cobalamin metabolism and transport
Homocystinuria with megaloblastic anemia
Cobalamin metabolism disorder
Homocystinuria, cbld type, variant 1
Methylmalonic aciduria and homocystinuria, cbld type
Methylmalonic aciduria, cbld type, variant 2
Advanced sleep phase syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Homocystinuria with megaloblastic anemia | 6 | 6 | 4 |
| Cobalamin metabolism disorder | 5 | 5 | 1 |
| Homocystinuria, cbld type, variant 1 | 5 | 5 | 1 |
| Inborn disorder of cobalamin metabolism and transport | 5 | 5 | 1 |
| Methylmalonic aciduria and homocystinuria, cbld type | 5 | 5 | 1 |
| Methylmalonic aciduria, cbld type, variant 2 | 5 | 5 | 1 |
| Advanced sleep phase syndrome | 1 | 1 | 4 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| MMADHC | 6 / 7 | Cobalamin metabolism disorder, Homocystinuria with megaloblastic anemia, Homocystinuria, cbld type, variant 1, Inborn disorder of cobalamin metabolism and transport and 2 more |
| PER3 | 2 / 7 | Advanced sleep phase syndrome, Homocystinuria with megaloblastic anemia |
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 ⇵ |
|---|---|---|---|---|---|
| Cobalamin transport and metabolism | KEGG | 3 / 18 | 286× | 9.86e-8 | 5.52e-6 ✓ sig. |
| Cobalamin (Cbl, vitamin B12) transport and metabolism | Reactome | 3 / 21 | 245× | 1.61e-7 | 8.44e-6 ✓ sig. |
| Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE | Reactome | 2 / 2 | 1,716× | 2.91e-7 | 1.42e-5 ✓ sig. |
| Defective MTR causes methylmalonic aciduria and homocystinuria type cblG | Reactome | 2 / 2 | 1,716× | 2.91e-7 | 1.42e-5 ✓ sig. |
| Circadian rhythm | KEGG | 3 / 34 | 151× | 7.20e-7 | 3.14e-5 ✓ sig. |
| Sulfur amino acid metabolism | Reactome | 2 / 6 | 572× | 4.36e-6 | 1.47e-4 ✓ sig. |
| Methylation | Reactome | 2 / 14 | 245× | 2.64e-5 | 6.54e-4 ✓ sig. |
| Defective MMADHC causes methylmalonic aciduria and homocystinuria type cblD | Reactome | 1 / 2 | 858× | 1.17e-3 | 1.27e-2 ✓ sig. |
| Circadian entrainment | KEGG | 2 / 97 | 35.4× | 1.32e-3 | 1.40e-2 ✓ sig. |
| Selenocompound metabolism | KEGG | 1 / 17 | 101× | 9.87e-3 | 5.65e-2 |
| Folate transport and metabolism | KEGG | 1 / 31 | 55.3× | 1.79e-2 | 8.05e-2 |
| One carbon pool by folate | KEGG | 1 / 38 | 45.2× | 2.19e-2 | 9.03e-2 |
| Cysteine and methionine metabolism | KEGG | 1 / 52 | 33.0× | 2.99e-2 | 1.08e-1 |
| Hedgehog signaling pathway | KEGG | 1 / 56 | 30.6× | 3.22e-2 | 1.13e-1 |
| Acute myeloid leukemia | KEGG | 1 / 68 | 25.2× | 3.90e-2 | 1.26e-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 ⇵ |
|---|---|---|---|---|---|
| cobalamin metabolic process | GO:0009235 | 3 / 9 | 890× | 2.70e-9 | 5.54e-7 ✓ sig. |
| rhythmic process | GO:0048511 | 4 / 148 | 72.2× | 1.30e-7 | 1.58e-5 ✓ sig. |
| regulation of circadian rhythm | GO:0042752 | 3 / 66 | 121× | 1.46e-6 | 1.17e-4 ✓ sig. |
| circadian regulation of gene expression | GO:0032922 | 3 / 67 | 120× | 1.53e-6 | 1.22e-4 ✓ sig. |
| circadian rhythm | GO:0007623 | 3 / 82 | 97.7× | 2.81e-6 | 1.99e-4 ✓ sig. |
| homocysteine metabolic process | GO:0050667 | 2 / 10 | 534× | 5.40e-6 | 3.36e-4 ✓ sig. |
| methionine biosynthetic process | GO:0009086 | 2 / 11 | 485× | 6.60e-6 | 3.94e-4 ✓ sig. |
| entrainment of circadian clock by photoperiod | GO:0043153 | 2 / 24 | 222× | 3.31e-5 | 1.35e-3 ✓ sig. |
| amino acid biosynthetic process | GO:0008652 | 2 / 27 | 198× | 4.20e-5 | 1.62e-3 ✓ sig. |
| sulfur amino acid metabolic process | GO:0000096 | 1 / 1 | 2,670× | 3.75e-4 | 7.81e-3 ✓ sig. |
| regulation of glutamate uptake involved in transmission of nerve impulse | GO:0051946 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| cellular response to bleomycin | GO:1904976 | 1 / 2 | 1,335× | 7.49e-4 | 1.23e-2 ✓ sig. |
| pteridine-containing compound metabolic process | GO:0042558 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| lactate biosynthetic process | GO:0019249 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |
| L-methionine salvage | GO:0071267 | 1 / 3 | 890× | 1.12e-3 | 1.55e-2 ✓ sig. |