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 305
6
Diseases
29
Unique genes
0.154
Avg. similarity score
Diabetes microvascular complications
Most-connected disease (5 links)
Disease
Searched: Transient ischemic attack
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Transient ischemic attack
Diabetes microvascular complications
Central nervous system disease
Esophageal stenosis
Paraneoplastic syndrome
Choroidal neovascularization
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Diabetes microvascular complications | 5 | 5 | 6 |
| Central nervous system disease | 4 | 4 | 4 |
| Esophageal stenosis | 2 | 2 | 1 |
| Paraneoplastic syndrome | 2 | 2 | 1 |
| Transient ischemic attack | 2 | 2 | 24 |
| Choroidal neovascularization | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| EPO | 4 / 6 | Central nervous system disease, Diabetes microvascular complications, Paraneoplastic syndrome, Transient ischemic attack |
| SOD2 | 4 / 6 | Central nervous system disease, Diabetes microvascular complications, Esophageal stenosis, Transient ischemic attack |
| IL1RN | 2 / 6 | Diabetes microvascular complications, Transient ischemic attack |
| VEGFA | 2 / 6 | Choroidal neovascularization, Diabetes microvascular complications |
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 ⇵ |
|---|---|---|---|---|---|
| Platinum drug resistance | KEGG | 4 / 75 | 22.1× | 2.96e-5 | 8.67e-4 ✓ sig. |
| Apoptosis - multiple species | KEGG | 3 / 32 | 38.8× | 5.99e-5 | 1.54e-3 ✓ sig. |
| Detoxification of Reactive Oxygen Species | Reactome | 3 / 34 | 36.5× | 7.20e-5 | 1.79e-3 ✓ sig. |
| Formation of apoptosome | Reactome | 2 / 6 | 138× | 8.39e-5 | 2.02e-3 ✓ sig. |
| Activation of caspases through apoptosome-mediated cleavage | Reactome | 2 / 6 | 138× | 8.39e-5 | 2.02e-3 ✓ sig. |
| Transcriptional activation of mitochondrial biogenesis | Reactome | 3 / 51 | 24.4× | 2.44e-4 | 4.68e-3 ✓ sig. |
| Regulation of the apoptosome activity | Reactome | 2 / 10 | 82.8× | 2.50e-4 | 4.77e-3 ✓ sig. |
| Regulation of gene expression by Hypoxia-inducible Factor | Reactome | 2 / 11 | 75.3× | 3.05e-4 | 5.61e-3 ✓ sig. |
| Apoptosis | KEGG | 4 / 137 | 12.1× | 3.08e-4 | 5.65e-3 ✓ sig. |
| Legionellosis | KEGG | 3 / 56 | 22.2× | 3.22e-4 | 5.85e-3 ✓ sig. |
| Endometrial cancer | KEGG | 3 / 59 | 21.1× | 3.76e-4 | 6.62e-3 ✓ sig. |
| VEGF signaling pathway | KEGG | 3 / 60 | 20.7× | 3.95e-4 | 6.88e-3 ✓ sig. |
| Cytokine-cytokine receptor interaction | KEGG | 5 / 298 | 6.9× | 6.62e-4 | 1.03e-2 ✓ sig. |
| JAK-STAT signaling pathway | KEGG | 4 / 168 | 9.9× | 6.68e-4 | 1.03e-2 ✓ sig. |
| Pancreatic cancer | KEGG | 3 / 77 | 16.1× | 8.21e-4 | 1.21e-2 ✓ 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 ⇵ |
|---|---|---|---|---|---|
| intrinsic apoptotic signaling pathway in response to DNA damage | GO:0008630 | 5 / 54 | 59.7× | 1.88e-8 | 2.96e-6 ✓ sig. |
| intrinsic apoptotic signaling pathway | GO:0097193 | 4 / 45 | 57.3× | 6.67e-7 | 6.07e-5 ✓ sig. |
| vasodilation | GO:0042311 | 4 / 50 | 51.6× | 1.03e-6 | 8.60e-5 ✓ sig. |
| apoptotic process | GO:0006915 | 9 / 747 | 7.8× | 1.21e-6 | 9.92e-5 ✓ sig. |
| release of cytochrome c from mitochondria | GO:0001836 | 3 / 23 | 84.0× | 5.83e-6 | 3.51e-4 ✓ sig. |
| response to hypoxia | GO:0001666 | 5 / 176 | 18.3× | 6.92e-6 | 4.03e-4 ✓ sig. |
| negative regulation of apoptotic process | GO:0043066 | 7 / 524 | 8.6× | 1.20e-5 | 6.21e-4 ✓ sig. |
| response to superoxide | GO:0000303 | 2 / 5 | 258× | 2.32e-5 | 1.04e-3 ✓ sig. |
| response to axon injury | GO:0048678 | 3 / 37 | 52.2× | 2.52e-5 | 1.10e-3 ✓ sig. |
| NADP+ biosynthetic process | GO:0006741 | 2 / 7 | 184× | 4.86e-5 | 1.82e-3 ✓ sig. |
| cytokine-mediated signaling pathway | GO:0019221 | 4 / 145 | 17.8× | 7.10e-5 | 2.42e-3 ✓ sig. |
| kidney development | GO:0001822 | 4 / 146 | 17.7× | 7.30e-5 | 2.47e-3 ✓ sig. |
| hydrogen peroxide biosynthetic process | GO:0050665 | 2 / 11 | 117× | 1.27e-4 | 3.72e-3 ✓ sig. |
| positive regulation of apoptotic process | GO:0043065 | 5 / 326 | 9.9× | 1.32e-4 | 3.84e-3 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 6 / 532 | 7.3× | 1.41e-4 | 4.03e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Diabetes microvascular complications | Transient ischemic attack | 0.107 | 3 | 6.63e-8 | 4.80e-7 ✓ sig. |
| Central nervous system disease | Diabetes microvascular complications | 0.222 | 2 | 7.59e-7 | 4.54e-6 ✓ sig. |
| Central nervous system disease | Transient ischemic attack | 0.074 | 2 | 1.39e-5 | 6.74e-5 ✓ sig. |
| Central nervous system disease | Paraneoplastic syndrome | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Central nervous system disease | Esophageal stenosis | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Choroidal neovascularization | Diabetes microvascular complications | 0.143 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |
| Diabetes microvascular complications | Esophageal stenosis | 0.143 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |
| Diabetes microvascular complications | Paraneoplastic syndrome | 0.143 | 1 | 3.90e-4 | 8.67e-4 ✓ sig. |