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 217
8
Diseases
12
Unique genes
0.228
Avg. similarity score
Tubular aggregate myopathy
Most-connected disease (7 links)
Disease
Searched: DPAGT1-congenital disorder of glycosylation
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DPAGT1-congenital disorder of glycosylation
Tubular aggregate myopathy
Caveolinopathy
Chromosome 3p25 monosomy
Creatine phosphokinase elevation
Rippling muscle disease
Vacuolar myopathy
combined immunodeficiency due to STIM1 deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Tubular aggregate myopathy | 7 | 7 | 7 |
| Caveolinopathy | 4 | 4 | 1 |
| Chromosome 3p25 monosomy | 4 | 4 | 3 |
| Creatine phosphokinase elevation | 4 | 4 | 1 |
| Rippling muscle disease | 4 | 4 | 3 |
| Vacuolar myopathy | 2 | 2 | 5 |
| combined immunodeficiency due to STIM1 deficiency | 2 | 2 | 1 |
| DPAGT1-congenital disorder of glycosylation | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CAV3 | 5 / 8 | Caveolinopathy, Chromosome 3p25 monosomy, Creatine phosphokinase elevation, Rippling muscle disease and 1 more |
| OXTR | 3 / 8 | Chromosome 3p25 monosomy, Rippling muscle disease, Tubular aggregate myopathy |
| STIM1 | 3 / 8 | combined immunodeficiency due to STIM1 deficiency, Tubular aggregate myopathy, Vacuolar myopathy |
| CASQ1 | 2 / 8 | Tubular aggregate myopathy, Vacuolar myopathy |
| DPAGT1 | 2 / 8 | DPAGT1-congenital disorder of glycosylation, Tubular aggregate myopathy |
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 ⇵ |
|---|---|---|---|---|---|
| Calcium signaling pathway | KEGG | 4 / 254 | 15.8× | 8.46e-5 | 2.03e-3 ✓ sig. |
| Defective GNE causes sialuria, Nonaka myopathy and inclusion body myopathy 2 | Reactome | 1 / 1 | 1,001× | 9.99e-4 | 1.40e-2 ✓ sig. |
| Defective DPAGT1 causes DPAGT1-CDG (CDG-1j) and CMSTA2 | Reactome | 1 / 1 | 1,001× | 9.99e-4 | 1.40e-2 ✓ sig. |
| Ion homeostasis | Reactome | 2 / 54 | 37.1× | 1.27e-3 | 1.69e-2 ✓ sig. |
| Vasopressin-like receptors | Reactome | 1 / 6 | 167× | 5.98e-3 | 5.11e-2 |
| Platelet activation | KEGG | 2 / 126 | 15.9× | 6.73e-3 | 5.51e-2 |
| Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | Reactome | 1 / 11 | 91.0× | 1.09e-2 | 7.50e-2 |
| Biosynthesis of various nucleotide sugars | KEGG | 1 / 15 | 66.7× | 1.49e-2 | 9.00e-2 |
| HSF1-dependent transactivation | Reactome | 1 / 19 | 52.7× | 1.88e-2 | 1.04e-1 |
| cAMP signaling pathway | KEGG | 2 / 226 | 8.9× | 2.05e-2 | 1.09e-1 |
| Cholesterol biosynthesis | Reactome | 1 / 21 | 47.7× | 2.08e-2 | 1.09e-1 |
| Terpenoid backbone biosynthesis | KEGG | 1 / 23 | 43.5× | 2.28e-2 | 1.15e-1 |
| Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | Reactome | 1 / 23 | 43.5× | 2.28e-2 | 1.15e-1 |
| Sialic acid metabolism | Reactome | 1 / 33 | 30.3× | 3.25e-2 | 1.40e-1 |
| Smooth Muscle Contraction | Reactome | 1 / 34 | 29.4× | 3.35e-2 | 1.42e-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 ⇵ |
|---|---|---|---|---|---|
| regulation of calcium ion transport | GO:0051924 | 3 / 25 | 187× | 4.62e-7 | 4.48e-5 ✓ sig. |
| positive regulation of adenylate cyclase activity | GO:0045762 | 2 / 5 | 623× | 3.78e-6 | 2.47e-4 ✓ sig. |
| store-operated calcium entry | GO:0002115 | 2 / 10 | 311× | 1.70e-5 | 8.15e-4 ✓ sig. |
| regulation of store-operated calcium entry | GO:2001256 | 2 / 14 | 222× | 3.43e-5 | 1.40e-3 ✓ sig. |
| calcium ion transport | GO:0006816 | 3 / 157 | 29.8× | 1.21e-4 | 3.59e-3 ✓ sig. |
| regulation of signal transduction by receptor internalization | GO:0038009 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| regulation of nerve growth factor receptor activity | GO:0051394 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| negative regulation of sarcomere organization | GO:0060299 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| negative regulation of membrane depolarization during cardiac muscle cell action potential | GO:1900826 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| positive regulation of store-operated calcium channel activity | GO:1901341 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| geranylgeranyl diphosphate biosynthetic process | GO:0033386 | 1 / 1 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| N-acetylglucosamine biosynthetic process | GO:0006045 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| geranyl diphosphate biosynthetic process | GO:0033384 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| farnesyl diphosphate biosynthetic process | GO:0045337 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| response to muscle inactivity | GO:0014870 | 1 / 2 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |