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 489
6
Diseases
6
Unique genes
0.317
Avg. similarity score
Quadriceps sparing myopathy
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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Quadriceps sparing myopathy
Sialuria
Thrombocytopenia 12 with or without myopathy
Vacuolar myopathy
Macrothrombocytopenia, isolated
Stormorken syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Quadriceps sparing myopathy | 4 | 4 | 1 |
| Sialuria | 4 | 4 | 1 |
| Thrombocytopenia 12 with or without myopathy | 4 | 4 | 1 |
| Vacuolar myopathy | 4 | 4 | 5 |
| Macrothrombocytopenia, isolated | 3 | 3 | 2 |
| Stormorken syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GNE | 5 / 6 | Macrothrombocytopenia, isolated, Quadriceps sparing myopathy, Sialuria, Thrombocytopenia 12 with or without myopathy and 1 more |
| STIM1 | 2 / 6 | Stormorken syndrome, Vacuolar 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 ⇵ |
|---|---|---|---|---|---|
| Ion homeostasis | Reactome | 2 / 54 | 74.1× | 2.94e-4 | 4.44e-3 ✓ sig. |
| Defective GNE causes sialuria, Nonaka myopathy and inclusion body myopathy 2 | Reactome | 1 / 1 | 2,002× | 5.00e-4 | 6.67e-3 ✓ sig. |
| Calcium signaling pathway | KEGG | 2 / 254 | 15.8× | 6.32e-3 | 4.25e-2 ✓ sig. |
| Biosynthesis of various nucleotide sugars | KEGG | 1 / 15 | 133× | 7.47e-3 | 4.73e-2 ✓ sig. |
| HSF1-dependent transactivation | Reactome | 1 / 19 | 105× | 9.46e-3 | 5.49e-2 |
| Antigen activates B Cell Receptor (BCR) leading to generation of second messengers | Reactome | 1 / 23 | 87.0× | 1.14e-2 | 6.18e-2 |
| TRP channels | Reactome | 1 / 28 | 71.5× | 1.39e-2 | 6.94e-2 |
| Sialic acid metabolism | Reactome | 1 / 33 | 60.7× | 1.64e-2 | 7.63e-2 |
| Biosynthesis of nucleotide sugars | KEGG | 1 / 37 | 54.1× | 1.83e-2 | 8.16e-2 |
| Processing of Capped Intron-Containing Pre-mRNA | Reactome | 1 / 37 | 54.1× | 1.83e-2 | 8.16e-2 |
| Amino sugar and nucleotide sugar metabolism | KEGG | 1 / 38 | 52.7× | 1.88e-2 | 8.28e-2 |
| Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation | Reactome | 1 / 38 | 52.7× | 1.88e-2 | 8.28e-2 |
| Mineral absorption | KEGG | 1 / 61 | 32.8× | 3.01e-2 | 1.08e-1 |
| Stimuli-sensing channels | Reactome | 1 / 79 | 25.3× | 3.88e-2 | 1.26e-1 |
| Platelet activation | KEGG | 1 / 126 | 15.9× | 6.13e-2 | 1.63e-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 store-operated calcium entry | GO:2001256 | 2 / 14 | 445× | 7.80e-6 | 4.51e-4 ✓ sig. |
| positive regulation of store-operated calcium channel activity | GO:1901341 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| calcium-dependent cell-matrix adhesion | GO:0016340 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| N-acetylglucosamine biosynthetic process | GO:0006045 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| response to muscle inactivity | GO:0014870 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| miRNA transport | GO:1990428 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| N-acetylneuraminate biosynthetic process | GO:0046380 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| calcium ion transport | GO:0006816 | 2 / 157 | 39.7× | 1.03e-3 | 1.49e-2 ✓ sig. |
| regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion | GO:0014809 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| UDP-N-acetylglucosamine metabolic process | GO:0006047 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| positive regulation of adenylate cyclase activity | GO:0045762 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| regulation of sequestering of calcium ion | GO:0051282 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| activation of store-operated calcium channel activity | GO:0032237 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| CMP-N-acetylneuraminate biosynthetic process | GO:0006055 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| positive regulation of telomere maintenance via telomere lengthening | GO:1904358 | 1 / 6 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Quadriceps sparing myopathy | Sialuria | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Quadriceps sparing myopathy | Thrombocytopenia 12 with or without myopathy | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Sialuria | Thrombocytopenia 12 with or without myopathy | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Macrothrombocytopenia, isolated | Sialuria | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Macrothrombocytopenia, isolated | Quadriceps sparing myopathy | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Macrothrombocytopenia, isolated | Thrombocytopenia 12 with or without myopathy | 0.333 | 1 | 1.29e-4 | 3.27e-4 ✓ sig. |
| Quadriceps sparing myopathy | Vacuolar myopathy | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Sialuria | Vacuolar myopathy | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Stormorken syndrome | Vacuolar myopathy | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Thrombocytopenia 12 with or without myopathy | Vacuolar myopathy | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |