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 423
5
Diseases
12
Unique genes
0.221
Avg. similarity score
Frontal lobe epilepsy
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Frontal lobe epilepsy
Nocturnal frontal lobe epilepsy
Childhood-onset epilepsy syndrome
familial sleep-related hypermotor epilepsy
Intracranial hypertension
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Frontal lobe epilepsy | 4 | 4 | 5 |
| Nocturnal frontal lobe epilepsy | 3 | 3 | 9 |
| Childhood-onset epilepsy syndrome | 2 | 2 | 3 |
| familial sleep-related hypermotor epilepsy | 2 | 2 | 3 |
| Intracranial hypertension | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CHRNA4 | 3 / 5 | familial sleep-related hypermotor epilepsy, Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy |
| CHRNB2 | 3 / 5 | familial sleep-related hypermotor epilepsy, Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy |
| KCNT1 | 3 / 5 | Childhood-onset epilepsy syndrome, Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy |
| CHRNA2 | 2 / 5 | familial sleep-related hypermotor epilepsy, Nocturnal frontal lobe epilepsy |
| CRH | 2 / 5 | Frontal lobe epilepsy, Nocturnal frontal lobe epilepsy |
| SLC4A10 | 2 / 5 | Frontal lobe epilepsy, Intracranial hypertension |
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 ⇵ |
|---|---|---|---|---|---|
| Highly calcium permeable nicotinic acetylcholine receptors | Reactome | 3 / 9 | 334× | 6.38e-8 | 4.43e-6 ✓ sig. |
| Highly calcium permeable postsynaptic nicotinic acetylcholine receptors | Reactome | 3 / 12 | 250× | 1.67e-7 | 1.02e-5 ✓ sig. |
| Nicotine addiction | KEGG | 3 / 41 | 73.2× | 7.95e-6 | 2.77e-4 ✓ sig. |
| Neuroactive ligand-receptor interaction | KEGG | 5 / 370 | 13.5× | 1.79e-5 | 5.46e-4 ✓ sig. |
| Highly sodium permeable postsynaptic acetylcholine nicotinic receptors | Reactome | 2 / 7 | 286× | 1.92e-5 | 5.78e-4 ✓ sig. |
| Amino acids regulate mTORC1 | Reactome | 2 / 55 | 36.4× | 1.32e-3 | 1.67e-2 ✓ sig. |
| Cholinergic synapse | KEGG | 2 / 115 | 17.4× | 5.63e-3 | 4.74e-2 ✓ sig. |
| Synthesis of UDP-N-acetyl-glucosamine | Reactome | 1 / 8 | 125× | 7.97e-3 | 5.96e-2 |
| Bicarbonate transporters | Reactome | 1 / 10 | 100× | 9.95e-3 | 6.82e-2 |
| GABA receptor activation | Reactome | 1 / 16 | 62.6× | 1.59e-2 | 9.02e-2 |
| Class B/2 (Secretin family receptors) | Reactome | 1 / 18 | 55.6× | 1.78e-2 | 9.67e-2 |
| Chemical carcinogenesis - receptor activation | KEGG | 2 / 215 | 9.3× | 1.87e-2 | 9.90e-2 |
| Ion channel transport | Reactome | 1 / 24 | 41.7× | 2.37e-2 | 1.13e-1 |
| Insulin receptor recycling | Reactome | 1 / 26 | 38.5× | 2.57e-2 | 1.18e-1 |
| Collecting duct acid secretion | KEGG | 1 / 28 | 35.7× | 2.76e-2 | 1.23e-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 ⇵ |
|---|---|---|---|---|---|
| monoatomic ion transport | GO:0006811 | 7 / 667 | 16.3× | 4.85e-8 | 6.61e-6 ✓ sig. |
| synaptic transmission, cholinergic | GO:0007271 | 3 / 25 | 187× | 4.62e-7 | 4.37e-5 ✓ sig. |
| acetylcholine receptor signaling pathway | GO:0095500 | 3 / 28 | 167× | 6.57e-7 | 5.88e-5 ✓ sig. |
| membrane depolarization | GO:0051899 | 3 / 32 | 146× | 9.93e-7 | 8.25e-5 ✓ sig. |
| response to nicotine | GO:0035094 | 3 / 40 | 117× | 1.97e-6 | 1.43e-4 ✓ sig. |
| monoatomic ion transmembrane transport | GO:0034220 | 5 / 404 | 19.3× | 3.22e-6 | 2.11e-4 ✓ sig. |
| regulation of postsynaptic membrane potential | GO:0060078 | 3 / 59 | 79.2× | 6.45e-6 | 3.67e-4 ✓ sig. |
| excitatory postsynaptic potential | GO:0060079 | 3 / 69 | 67.7× | 1.04e-5 | 5.35e-4 ✓ sig. |
| response to acetylcholine | GO:1905144 | 2 / 8 | 389× | 1.06e-5 | 5.43e-4 ✓ sig. |
| chemical synaptic transmission | GO:0007268 | 4 / 236 | 26.4× | 1.13e-5 | 5.74e-4 ✓ sig. |
| behavioral response to nicotine | GO:0035095 | 2 / 9 | 346× | 1.36e-5 | 6.62e-4 ✓ sig. |
| regulation of dopamine secretion | GO:0014059 | 2 / 15 | 208× | 3.95e-5 | 1.51e-3 ✓ sig. |
| locomotory exploration behavior | GO:0035641 | 2 / 16 | 195× | 4.51e-5 | 1.67e-3 ✓ sig. |
| neuromuscular synaptic transmission | GO:0007274 | 2 / 31 | 100× | 1.74e-4 | 4.58e-3 ✓ sig. |
| response to cocaine | GO:0042220 | 2 / 35 | 89.0× | 2.22e-4 | 5.43e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Frontal lobe epilepsy | Nocturnal frontal lobe epilepsy | 0.364 | 4 | 2.69e-13 | 3.62e-12 ✓ sig. |
| familial sleep-related hypermotor epilepsy | Nocturnal frontal lobe epilepsy | 0.300 | 3 | 1.38e-10 | 1.43e-9 ✓ sig. |
| familial sleep-related hypermotor epilepsy | Frontal lobe epilepsy | 0.286 | 2 | 2.53e-7 | 1.75e-6 ✓ sig. |
| Frontal lobe epilepsy | Intracranial hypertension | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Childhood-onset epilepsy syndrome | Frontal lobe epilepsy | 0.125 | 1 | 9.74e-4 | 1.64e-3 ✓ sig. |
| Childhood-onset epilepsy syndrome | Nocturnal frontal lobe epilepsy | 0.083 | 1 | 1.75e-3 | 2.59e-3 ✓ sig. |