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 516
5
Diseases
6
Unique genes
0.248
Avg. similarity score
Dopa-responsive dystonia
Most-connected disease (4 links)
Disease
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Dopa-responsive dystonia
Dystonia, dopa-responsive, with or without hyperphenylalaninemia
GTP cyclohydrolase I deficiency
Hyperphenylalaninemia, bh4-deficient, b
Sepiapterin reductase deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Dopa-responsive dystonia | 4 | 4 | 4 |
| Dystonia, dopa-responsive, with or without hyperphenylalaninemia | 4 | 4 | 4 |
| GTP cyclohydrolase I deficiency | 3 | 3 | 1 |
| Hyperphenylalaninemia, bh4-deficient, b | 3 | 3 | 1 |
| Sepiapterin reductase deficiency | 2 | 2 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| GCH1 | 4 / 5 | Dopa-responsive dystonia, Dystonia, dopa-responsive, with or without hyperphenylalaninemia, GTP cyclohydrolase I deficiency, Hyperphenylalaninemia, bh4-deficient, b |
| SPR | 3 / 5 | Dopa-responsive dystonia, Dystonia, dopa-responsive, with or without hyperphenylalaninemia, Sepiapterin reductase deficiency |
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 ⇵ |
|---|---|---|---|---|---|
| Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation | Reactome | 2 / 11 | 364× | 1.14e-5 | 3.25e-4 ✓ sig. |
| Folate biosynthesis | KEGG | 2 / 28 | 143× | 7.82e-5 | 1.56e-3 ✓ sig. |
| Signaling by Insulin receptor | Reactome | 1 / 2 | 1,001× | 9.99e-4 | 1.13e-2 ✓ sig. |
| Biosynthesis of cofactors | KEGG | 2 / 154 | 26.0× | 2.37e-3 | 2.16e-2 ✓ sig. |
| IRS activation | Reactome | 1 / 5 | 400× | 2.50e-3 | 2.23e-2 ✓ sig. |
| Insulin receptor signalling cascade | Reactome | 1 / 6 | 334× | 2.99e-3 | 2.54e-2 ✓ sig. |
| FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Signal attenuation | Reactome | 1 / 10 | 200× | 4.99e-3 | 3.64e-2 ✓ sig. |
| Purine ribonucleoside monophosphate biosynthesis | Reactome | 1 / 12 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| Pregnenolone biosynthesis | Reactome | 1 / 12 | 167× | 5.98e-3 | 4.10e-2 ✓ sig. |
| eNOS activation | Reactome | 1 / 13 | 154× | 6.48e-3 | 4.32e-2 ✓ sig. |
| Insulin processing | Reactome | 1 / 14 | 143× | 6.98e-3 | 4.53e-2 ✓ sig. |
| Acetylcholine Neurotransmitter Release Cycle | Reactome | 1 / 17 | 118× | 8.46e-3 | 5.13e-2 |
| Serotonin Neurotransmitter Release Cycle | Reactome | 1 / 18 | 111× | 8.96e-3 | 5.31e-2 |
| Norepinephrine Neurotransmitter Release Cycle | Reactome | 1 / 18 | 111× | 8.96e-3 | 5.31e-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 ⇵ |
|---|---|---|---|---|---|
| positive regulation of nitric-oxide synthase activity | GO:0051000 | 2 / 3 | 2,076× | 2.58e-7 | 2.79e-5 ✓ sig. |
| tetrahydrobiopterin biosynthetic process | GO:0006729 | 2 / 8 | 779× | 2.40e-6 | 1.76e-4 ✓ sig. |
| dopamine biosynthetic process | GO:0042416 | 2 / 9 | 692× | 3.09e-6 | 2.15e-4 ✓ sig. |
| nitric oxide biosynthetic process | GO:0006809 | 2 / 23 | 271× | 2.17e-5 | 9.82e-4 ✓ sig. |
| pteridine-containing compound biosynthetic process | GO:0042559 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| general adaptation syndrome | GO:0051866 | 1 / 1 | 3,115× | 3.21e-4 | 7.04e-3 ✓ sig. |
| regulation of lung blood pressure | GO:0014916 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| negative regulation of glycogen catabolic process | GO:0045818 | 1 / 2 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| pteridine-containing compound metabolic process | GO:0042558 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| habenula development | GO:0021986 | 1 / 3 | 1,038× | 9.63e-4 | 1.42e-2 ✓ sig. |
| tetrahydrobiopterin metabolic process | GO:0046146 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| positive regulation of nitric oxide mediated signal transduction | GO:0010750 | 1 / 4 | 779× | 1.28e-3 | 1.67e-2 ✓ sig. |
| positive regulation of dendritic spine maintenance | GO:1902952 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| negative regulation of respiratory burst involved in inflammatory response | GO:0060266 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
| cellular response to corticotropin-releasing hormone stimulus | GO:0071376 | 1 / 5 | 623× | 1.60e-3 | 1.88e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Dopa-responsive dystonia | Dystonia, dopa-responsive, with or without hyperphenylalaninemia | 0.286 | 2 | 3.00e-7 | 1.96e-6 ✓ sig. |
| GTP cyclohydrolase I deficiency | Hyperphenylalaninemia, bh4-deficient, b | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Dopa-responsive dystonia | GTP cyclohydrolase I deficiency | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Dopa-responsive dystonia | Hyperphenylalaninemia, bh4-deficient, b | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Dystonia, dopa-responsive, with or without hyperphenylalaninemia | GTP cyclohydrolase I deficiency | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Dystonia, dopa-responsive, with or without hyperphenylalaninemia | Hyperphenylalaninemia, bh4-deficient, b | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Dystonia, dopa-responsive, with or without hyperphenylalaninemia | Sepiapterin reductase deficiency | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Dopa-responsive dystonia | Sepiapterin reductase deficiency | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |