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 463
6
Diseases
102
Unique genes
0.157
Avg. similarity score
Chagas cardiomyopathy
Most-connected disease (5 links)
Disease
Searched: Craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature (cousin syndrome)
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature (cousin syndrome)
Chagas cardiomyopathy
Cousin syndrome
Obstructive sleep apnea syndrome
Pelviscapular dysplasia
Neurodevelopmental disorder with language delay and seizures
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Chagas cardiomyopathy | 5 | 5 | 25 |
| Cousin syndrome | 4 | 4 | 1 |
| Craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature (cousin syndrome) | 4 | 4 | 1 |
| Obstructive sleep apnea syndrome | 4 | 4 | 81 |
| Pelviscapular dysplasia | 4 | 4 | 1 |
| Neurodevelopmental disorder with language delay and seizures | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TBX15 | 5 / 6 | Chagas cardiomyopathy, Cousin syndrome, Craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature (cousin syndrome), Obstructive sleep apnea syndrome and 1 more |
| GPR83 | 2 / 6 | Chagas cardiomyopathy, Obstructive sleep apnea syndrome |
| IZUMO1R | 2 / 6 | Chagas cardiomyopathy, Obstructive sleep apnea syndrome |
| NRG1 | 2 / 6 | Chagas cardiomyopathy, Obstructive sleep apnea syndrome |
| TIAM1 | 2 / 6 | Chagas cardiomyopathy, Neurodevelopmental disorder with language delay and seizures |
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)
None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Defective SLCO1B1 causes hyperbilirubinemia, Rotor type (HBLRR) | Reactome | 1 / 1 | 118× | 8.49e-3 | 5.14e-2 |
| Reversal of alkylation damage by DNA dioxygenases | Reactome | 1 / 2 | 58.9× | 1.69e-2 | 7.79e-2 |
| Activation and oligomerization of BAK protein | Reactome | 1 / 2 | 58.9× | 1.69e-2 | 7.79e-2 |
| Clathrin-mediated endocytosis | Reactome | 4 / 130 | 3.6× | 2.47e-2 | 9.67e-2 |
| Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) | Reactome | 1 / 3 | 39.2× | 2.53e-2 | 9.80e-2 |
| TCF7L2 mutants don't bind CTBP | Reactome | 1 / 3 | 39.2× | 2.53e-2 | 9.80e-2 |
| Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors | Reactome | 1 / 3 | 39.2× | 2.53e-2 | 9.80e-2 |
| Adherens junctions interactions | Reactome | 2 / 32 | 7.4× | 3.00e-2 | 1.08e-1 |
| Neurophilin interactions with VEGF and VEGFR | Reactome | 1 / 4 | 29.4× | 3.35e-2 | 1.15e-1 |
| Thyroid cancer | KEGG | 2 / 37 | 6.4× | 3.92e-2 | 1.26e-1 |
| GRB7 events in ERBB2 signaling | Reactome | 1 / 5 | 23.5× | 4.18e-2 | 1.31e-1 |
| Chylomicron clearance | Reactome | 1 / 5 | 23.5× | 4.18e-2 | 1.31e-1 |
| Release of apoptotic factors from the mitochondria | Reactome | 1 / 5 | 23.5× | 4.18e-2 | 1.31e-1 |
| Beta defensins | Reactome | 2 / 40 | 5.9× | 4.52e-2 | 1.37e-1 |
| Defensins | Reactome | 2 / 42 | 5.6× | 4.94e-2 | 1.44e-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 ⇵ |
|---|---|---|---|---|---|
| negative regulation of type B pancreatic cell apoptotic process | GO:2000675 | 2 / 6 | 61.1× | 4.36e-4 | 8.66e-3 ✓ sig. |
| negative regulation of endoplasmic reticulum calcium ion concentration | GO:0032471 | 2 / 6 | 61.1× | 4.36e-4 | 8.66e-3 ✓ sig. |
| nitric oxide-cGMP-mediated signaling | GO:0038060 | 2 / 10 | 36.6× | 1.29e-3 | 1.67e-2 ✓ sig. |
| regulation of Cdc42 protein signal transduction | GO:0032489 | 2 / 12 | 30.5× | 1.88e-3 | 2.06e-2 ✓ sig. |
| positive regulation of membrane protein ectodomain proteolysis | GO:0051044 | 2 / 17 | 21.6× | 3.80e-3 | 2.93e-2 ✓ sig. |
| regulation of dendrite development | GO:0050773 | 2 / 17 | 21.6× | 3.80e-3 | 2.93e-2 ✓ sig. |
| cellular response to unfolded protein | GO:0034620 | 2 / 18 | 20.4× | 4.26e-3 | 3.09e-2 ✓ sig. |
| actin filament capping | GO:0051693 | 2 / 19 | 19.3× | 4.75e-3 | 3.27e-2 ✓ sig. |
| lipid transport involved in lipid storage | GO:0010877 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |
| maintenance of location in cell | GO:0051651 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |
| intermediate-density lipoprotein particle clearance | GO:0071831 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |
| negative regulation of postsynaptic membrane organization | GO:1901627 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |
| negative regulation of phospholipid efflux | GO:1902999 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |
| negative regulation of lipid transport across blood-brain barrier | GO:1903001 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |
| positive regulation of lipid transport across blood-brain barrier | GO:1903002 | 1 / 1 | 183× | 5.46e-3 | 3.47e-2 ✓ sig. |