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 133
11
Diseases
32
Unique genes
0.140
Avg. similarity score
Methylmalonic acidemia
Most-connected disease (9 links)
Disease
Searched: Methylmalonic acidemia with homocystinuria, type cblJ
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Methylmalonic acidemia with homocystinuria, type cblJ
Methylmalonic acidemia
Cobalamin c disease
Intracellular cobalamin metabolism disorder
Methylmalonic aciduria and homocystinuria
Methylmalonic aciduria and homocystinuria type cblF
Donnai-barrow syndrome
Methylmalonic aciduria and homocystinuria, cblc type
Methylmalonic acidemia due to methylmalonyl-CoA epimerase deficiency
Methylmalonic aciduria, vitamin b12-responsive
Short stature and microcephaly with genital anomalies
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Methylmalonic acidemia | 9 | 9 | 28 |
| Cobalamin c disease | 7 | 7 | 7 |
| Intracellular cobalamin metabolism disorder | 7 | 7 | 9 |
| Methylmalonic aciduria and homocystinuria | 5 | 5 | 3 |
| Methylmalonic aciduria and homocystinuria type cblF | 5 | 5 | 1 |
| Donnai-barrow syndrome | 4 | 4 | 2 |
| Methylmalonic acidemia with homocystinuria, type cblJ | 3 | 3 | 1 |
| Methylmalonic aciduria and homocystinuria, cblc type | 3 | 3 | 1 |
| Methylmalonic acidemia due to methylmalonyl-CoA epimerase deficiency | 1 | 1 | 1 |
| Methylmalonic aciduria, vitamin b12-responsive | 1 | 1 | 1 |
| Short stature and microcephaly with genital anomalies | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| LMBRD1 | 6 / 11 | Cobalamin c disease, Donnai-barrow syndrome, Intracellular cobalamin metabolism disorder, Methylmalonic acidemia and 2 more |
| ABCD4 | 4 / 11 | Cobalamin c disease, Intracellular cobalamin metabolism disorder, Methylmalonic acidemia, Methylmalonic acidemia with homocystinuria, type cblJ |
| MMACHC | 4 / 11 | Cobalamin c disease, Intracellular cobalamin metabolism disorder, Methylmalonic acidemia, Methylmalonic aciduria and homocystinuria, cblc type |
| HCFC1 | 3 / 11 | Cobalamin c disease, Intracellular cobalamin metabolism disorder, Methylmalonic acidemia |
| MMADHC | 3 / 11 | Cobalamin c disease, Intracellular cobalamin metabolism disorder, Methylmalonic acidemia |
| THAP11 | 3 / 11 | Intracellular cobalamin metabolism disorder, Methylmalonic acidemia, Methylmalonic aciduria and homocystinuria |
| ZNF143 | 3 / 11 | Intracellular cobalamin metabolism disorder, Methylmalonic acidemia, Methylmalonic aciduria and homocystinuria |
| CENPT | 2 / 11 | Methylmalonic acidemia, Short stature and microcephaly with genital anomalies |
| LINC02491 | 2 / 11 | Methylmalonic acidemia, Methylmalonic aciduria, vitamin b12-responsive |
| MCEE | 2 / 11 | Methylmalonic acidemia, Methylmalonic acidemia due to methylmalonyl-CoA epimerase deficiency |
| PRDX1 | 2 / 11 | Cobalamin c disease, Methylmalonic acidemia |
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 | 14 / 18 | 292× | 9.70e-35 | 4.43e-31 ✓ sig. |
| Cobalamin (Cbl, vitamin B12) transport and metabolism | Reactome | 10 / 21 | 179× | 1.30e-21 | 1.27e-18 ✓ sig. |
| Propionyl-CoA catabolism | Reactome | 3 / 5 | 225× | 1.71e-7 | 8.92e-6 ✓ sig. |
| Peroxisome | KEGG | 5 / 83 | 22.6× | 2.43e-6 | 8.90e-5 ✓ sig. |
| Defective MMAA causes methylmalonic aciduria type cblA | Reactome | 2 / 2 | 375× | 6.88e-6 | 2.14e-4 ✓ sig. |
| Defective MUT causes methylmalonic aciduria mut type | Reactome | 2 / 2 | 375× | 6.88e-6 | 2.14e-4 ✓ sig. |
| Defective MMADHC causes methylmalonic aciduria and homocystinuria type cblD | Reactome | 2 / 2 | 375× | 6.88e-6 | 2.14e-4 ✓ sig. |
| Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE | Reactome | 2 / 2 | 375× | 6.88e-6 | 2.14e-4 ✓ sig. |
| Defective MTR causes methylmalonic aciduria and homocystinuria type cblG | Reactome | 2 / 2 | 375× | 6.88e-6 | 2.14e-4 ✓ sig. |
| Vitamin digestion and absorption | KEGG | 3 / 26 | 43.3× | 4.29e-5 | 9.68e-4 ✓ sig. |
| Propanoate metabolism | KEGG | 3 / 32 | 35.2× | 8.09e-5 | 1.60e-3 ✓ sig. |
| Detoxification of Reactive Oxygen Species | Reactome | 3 / 34 | 33.1× | 9.72e-5 | 1.85e-3 ✓ sig. |
| Sulfur amino acid metabolism | Reactome | 2 / 6 | 125× | 1.02e-4 | 1.93e-3 ✓ sig. |
| Valine, leucine and isoleucine degradation | KEGG | 3 / 48 | 23.5× | 2.74e-4 | 4.20e-3 ✓ sig. |
| Transcriptional activation of mitochondrial biogenesis | Reactome | 3 / 51 | 22.1× | 3.28e-4 | 4.82e-3 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| cobalamin metabolic process | GO:0009235 | 7 / 9 | 454× | 7.67e-19 | 1.03e-15 ✓ sig. |
| cobalamin transport | GO:0015889 | 3 / 9 | 195× | 3.80e-7 | 3.86e-5 ✓ sig. |
| homocysteine metabolic process | GO:0050667 | 3 / 10 | 175× | 5.43e-7 | 5.23e-5 ✓ sig. |
| methionine biosynthetic process | GO:0009086 | 2 / 11 | 106× | 1.55e-4 | 4.24e-3 ✓ sig. |
| removal of superoxide radicals | GO:0019430 | 2 / 15 | 77.9× | 2.94e-4 | 6.68e-3 ✓ sig. |
| response to reactive oxygen species | GO:0000302 | 2 / 20 | 58.4× | 5.29e-4 | 9.88e-3 ✓ sig. |
| cytoskeleton-dependent cytokinesis | GO:0061640 | 2 / 21 | 55.6× | 5.85e-4 | 1.06e-2 ✓ sig. |
| peroxisome organization | GO:0007031 | 2 / 23 | 50.8× | 7.03e-4 | 1.19e-2 ✓ sig. |
| amino acid biosynthetic process | GO:0008652 | 2 / 27 | 43.3× | 9.71e-4 | 1.43e-2 ✓ sig. |
| diol metabolic process | GO:0034311 | 1 / 1 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| regulation of L-glutamate import across plasma membrane | GO:0002036 | 1 / 1 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure | GO:0003069 | 1 / 1 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| erythrophore differentiation | GO:0048773 | 1 / 1 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| response to magnetism | GO:0071000 | 1 / 1 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| regulation of vitamin metabolic process | GO:0030656 | 1 / 1 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |