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 258
7
Diseases
4
Unique genes
0.526
Avg. similarity score
Aphasia
Most-connected disease (6 links)
Disease
Searched: Cardiac tamponade
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Cardiac tamponade
Aphasia
Commisural aphasia
Dejerine-lichtheim phenomenon
Postictal aphasia
Dysphasia
Syntactic aphasia
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Aphasia | 6 | 6 | 2 |
| Commisural aphasia | 6 | 6 | 2 |
| Dejerine-lichtheim phenomenon | 6 | 6 | 2 |
| Postictal aphasia | 6 | 6 | 2 |
| Dysphasia | 5 | 5 | 4 |
| Syntactic aphasia | 5 | 5 | 2 |
| Cardiac tamponade | 4 | 4 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| PLAT | 7 / 7 | Aphasia, Cardiac tamponade, Commisural aphasia, Dejerine-lichtheim phenomenon and 3 more |
| L1CAM | 6 / 7 | Aphasia, Commisural aphasia, Dejerine-lichtheim phenomenon, Dysphasia and 2 more |
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 ⇵ |
|---|---|---|---|---|---|
| L1CAM interactions | Reactome | 1 / 4 | 751× | 1.33e-3 | 1.75e-2 ✓ sig. |
| MECP2 regulates neuronal receptors and channels | Reactome | 1 / 4 | 751× | 1.33e-3 | 1.75e-2 ✓ sig. |
| Interaction between L1 and Ankyrins | Reactome | 1 / 13 | 231× | 4.32e-3 | 4.10e-2 ✓ sig. |
| Dissolution of Fibrin Clot | Reactome | 1 / 13 | 231× | 4.32e-3 | 4.10e-2 ✓ sig. |
| Toll Like Receptor 4 (TLR4) Cascade | Reactome | 1 / 19 | 158× | 6.31e-3 | 5.30e-2 |
| Interleukin-37 signaling | Reactome | 1 / 21 | 143× | 6.98e-3 | 5.64e-2 |
| Signal transduction by L1 | Reactome | 1 / 21 | 143× | 6.98e-3 | 5.64e-2 |
| Proximal tubule bicarbonate reclamation | KEGG | 1 / 23 | 131× | 7.64e-3 | 5.97e-2 |
| Basigin interactions | Reactome | 1 / 25 | 120× | 8.30e-3 | 6.28e-2 |
| Signaling by PDGF | Reactome | 1 / 33 | 91.0× | 1.09e-2 | 7.50e-2 |
| Aldosterone-regulated sodium reabsorption | KEGG | 1 / 38 | 79.0× | 1.26e-2 | 8.17e-2 |
| Recycling pathway of L1 | Reactome | 1 / 40 | 75.1× | 1.33e-2 | 8.41e-2 |
| Carbohydrate digestion and absorption | KEGG | 1 / 48 | 62.6× | 1.59e-2 | 9.38e-2 |
| Endocrine and other factor-regulated calcium reabsorption | KEGG | 1 / 53 | 56.7× | 1.75e-2 | 9.95e-2 |
| Ion homeostasis | Reactome | 1 / 54 | 55.6× | 1.79e-2 | 1.00e-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 ⇵ |
|---|---|---|---|---|---|
| olfactory cortex development | GO:0021989 | 1 / 1 | 4,672× | 2.14e-4 | 5.46e-3 ✓ sig. |
| regulation of glutamate uptake involved in transmission of nerve impulse | GO:0051946 | 1 / 2 | 2,336× | 4.28e-4 | 8.87e-3 ✓ sig. |
| negative regulation of striated muscle contraction | GO:0045988 | 1 / 3 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| negative regulation of calcium ion transmembrane transport | GO:1903170 | 1 / 3 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| trans-synaptic signaling by BDNF, modulating synaptic transmission | GO:0099183 | 1 / 3 | 1,557× | 6.42e-4 | 1.16e-2 ✓ sig. |
| amygdala development | GO:0021764 | 1 / 4 | 1,168× | 8.56e-4 | 1.41e-2 ✓ sig. |
| negative regulation of heart contraction | GO:0045822 | 1 / 6 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| response to glycoside | GO:1903416 | 1 / 6 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| prevention of polyspermy | GO:0060468 | 1 / 6 | 779× | 1.28e-3 | 1.80e-2 ✓ sig. |
| negative regulation of plasminogen activation | GO:0010757 | 1 / 7 | 667× | 1.50e-3 | 1.98e-2 ✓ sig. |
| response to potassium ion | GO:0035864 | 1 / 8 | 584× | 1.71e-3 | 2.14e-2 ✓ sig. |
| regulation of striated muscle contraction | GO:0006942 | 1 / 8 | 584× | 1.71e-3 | 2.14e-2 ✓ sig. |
| fear response | GO:0042596 | 1 / 8 | 584× | 1.71e-3 | 2.14e-2 ✓ sig. |
| positive regulation of heart contraction | GO:0045823 | 1 / 9 | 519× | 1.93e-3 | 2.28e-2 ✓ sig. |
| smooth muscle cell migration | GO:0014909 | 1 / 9 | 519× | 1.93e-3 | 2.28e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Commisural aphasia | Postictal aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Postictal aphasia | Syntactic aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Dejerine-lichtheim phenomenon | Syntactic aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Dejerine-lichtheim phenomenon | Postictal aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Commisural aphasia | Syntactic aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Commisural aphasia | Dejerine-lichtheim phenomenon | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Aphasia | Postictal aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Aphasia | Syntactic aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Aphasia | Dejerine-lichtheim phenomenon | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Aphasia | Commisural aphasia | 0.667 | 2 | 8.44e-9 | 6.82e-8 ✓ sig. |
| Aphasia | Dysphasia | 0.400 | 2 | 5.06e-8 | 3.71e-7 ✓ sig. |
| Commisural aphasia | Dysphasia | 0.400 | 2 | 5.06e-8 | 3.71e-7 ✓ sig. |
| Dejerine-lichtheim phenomenon | Dysphasia | 0.400 | 2 | 5.06e-8 | 3.71e-7 ✓ sig. |
| Dysphasia | Postictal aphasia | 0.400 | 2 | 5.06e-8 | 3.71e-7 ✓ sig. |
| Dysphasia | Syntactic aphasia | 0.400 | 2 | 5.06e-8 | 3.71e-7 ✓ sig. |
| Cardiac tamponade | Commisural aphasia | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Cardiac tamponade | Dejerine-lichtheim phenomenon | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Cardiac tamponade | Postictal aphasia | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |
| Aphasia | Cardiac tamponade | 0.333 | 1 | 1.30e-4 | 3.93e-4 ✓ sig. |