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 389
5
Diseases
10
Unique genes
0.227
Avg. similarity score
Pyridoxine dependent epilepsy
Most-connected disease (4 links)
Disease
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Pyridoxine dependent epilepsy
Continuous spike and wave during sleep syndrome
Continuous spike and wave during slow wave sleep syndrome
Focal epilepsy with speech disorder and impaired intellectual development
Amelocerebrohypohidrotic syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Pyridoxine dependent epilepsy | 4 | 4 | 8 |
| Continuous spike and wave during sleep syndrome | 3 | 3 | 1 |
| Continuous spike and wave during slow wave sleep syndrome | 3 | 3 | 2 |
| Focal epilepsy with speech disorder and impaired intellectual development | 3 | 3 | 1 |
| Amelocerebrohypohidrotic syndrome | 1 | 1 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GRIN2A | 4 / 5 | Continuous spike and wave during sleep syndrome, Continuous spike and wave during slow wave sleep syndrome, Focal epilepsy with speech disorder and impaired intellectual development, Pyridoxine dependent epilepsy |
| SLC13A5 | 2 / 5 | Amelocerebrohypohidrotic syndrome, Pyridoxine dependent epilepsy |
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 ⇵ |
|---|---|---|---|---|---|
| beta-Alanine metabolism | KEGG | 2 / 31 | 77.5× | 2.86e-4 | 5.18e-3 ✓ sig. |
| GABA synthesis | Reactome | 1 / 2 | 601× | 1.66e-3 | 2.00e-2 ✓ sig. |
| Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 | Reactome | 1 / 3 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 | Reactome | 1 / 3 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Sodium-coupled sulphate, di- and tri-carboxylate transporters | Reactome | 1 / 5 | 240× | 4.16e-3 | 3.87e-2 ✓ sig. |
| Assembly and cell surface presentation of NMDA receptors | Reactome | 1 / 6 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| Choline catabolism | Reactome | 1 / 6 | 200× | 4.99e-3 | 4.37e-2 ✓ sig. |
| APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway | Reactome | 1 / 7 | 172× | 5.82e-3 | 4.84e-2 ✓ sig. |
| O-linked glycosylation | Reactome | 1 / 10 | 120× | 8.30e-3 | 6.10e-2 |
| Lysine catabolism | Reactome | 1 / 12 | 100× | 9.95e-3 | 6.82e-2 |
| GABA synthesis, release, reuptake and degradation | Reactome | 1 / 13 | 92.4× | 1.08e-2 | 7.19e-2 |
| Taurine and hypotaurine metabolism | KEGG | 1 / 17 | 70.6× | 1.41e-2 | 8.38e-2 |
| Synaptic adhesion-like molecules | Reactome | 1 / 21 | 57.2× | 1.74e-2 | 9.50e-2 |
| Histidine metabolism | KEGG | 1 / 22 | 54.6× | 1.82e-2 | 9.77e-2 |
| Unblocking of NMDA receptors, glutamate binding and activation | Reactome | 1 / 22 | 54.6× | 1.82e-2 | 9.77e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| memory | GO:0007613 | 3 / 87 | 64.4× | 1.14e-5 | 5.77e-4 ✓ sig. |
| locomotion | GO:0040011 | 2 / 12 | 311× | 1.70e-5 | 7.89e-4 ✓ sig. |
| sodium ion transmembrane transport | GO:0035725 | 3 / 134 | 41.8× | 4.17e-5 | 1.57e-3 ✓ sig. |
| tricarboxylic acid transport | GO:0006842 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| succinate transport | GO:0015744 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| tricarboxylic acid transmembrane transport | GO:0035674 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| vitamin B6 metabolic process | GO:0042816 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| intrinsic apoptotic signaling pathway in response to osmotic stress | GO:0008627 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| gamma-aminobutyrate shunt | GO:0006540 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| oxaloacetate transport | GO:0015729 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| fumarate transport | GO:0015741 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| glycine betaine biosynthetic process from choline | GO:0019285 | 1 / 2 | 934× | 1.07e-3 | 1.57e-2 ✓ sig. |
| neurogenesis | GO:0022008 | 2 / 102 | 36.6× | 1.29e-3 | 1.75e-2 ✓ sig. |
| directional locomotion | GO:0033058 | 1 / 3 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
| protein localization to postsynaptic membrane | GO:1903539 | 1 / 3 | 623× | 1.60e-3 | 1.98e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Continuous spike and wave during sleep syndrome | Focal epilepsy with speech disorder and impaired intellectual development | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Continuous spike and wave during sleep syndrome | Continuous spike and wave during slow wave sleep syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Continuous spike and wave during slow wave sleep syndrome | Focal epilepsy with speech disorder and impaired intellectual development | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Continuous spike and wave during sleep syndrome | Pyridoxine dependent epilepsy | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Focal epilepsy with speech disorder and impaired intellectual development | Pyridoxine dependent epilepsy | 0.111 | 1 | 5.20e-4 | 1.04e-3 ✓ sig. |
| Amelocerebrohypohidrotic syndrome | Pyridoxine dependent epilepsy | 0.100 | 1 | 1.04e-3 | 1.72e-3 ✓ sig. |
| Continuous spike and wave during slow wave sleep syndrome | Pyridoxine dependent epilepsy | 0.100 | 1 | 1.04e-3 | 1.72e-3 ✓ sig. |