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 332
6
Diseases
9
Unique genes
0.288
Avg. similarity score
Cerebellar ataxia with deafness and narcolepsy
Most-connected disease (4 links)
Disease
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Cerebellar ataxia with deafness and narcolepsy
Cerebellar ataxia, deafness, and narcolepsy
Dominantly inherited sensory neuropathy
autosomal dominant cerebellar ataxia, deafness and narcolepsy
Cerebral atrophy
hereditary sensory and autonomic neuropathy type 6
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cerebellar ataxia with deafness and narcolepsy | 4 | 4 | 1 |
| Cerebellar ataxia, deafness, and narcolepsy | 4 | 4 | 1 |
| Dominantly inherited sensory neuropathy | 4 | 4 | 3 |
| autosomal dominant cerebellar ataxia, deafness and narcolepsy | 4 | 4 | 1 |
| Cerebral atrophy | 3 | 3 | 7 |
| hereditary sensory and autonomic neuropathy type 6 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| DNMT1 | 5 / 6 | autosomal dominant cerebellar ataxia, deafness and narcolepsy, Cerebellar ataxia with deafness and narcolepsy, Cerebellar ataxia, deafness, and narcolepsy, Cerebral atrophy and 1 more |
| DST | 2 / 6 | Dominantly inherited sensory neuropathy, hereditary sensory and autonomic neuropathy type 6 |
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 ⇵ |
|---|---|---|---|---|---|
| Defective PMM2 causes PMM2-CDG (CDG-1a) | Reactome | 1 / 1 | 1,334× | 7.49e-4 | 1.09e-2 ✓ sig. |
| Synthesis of GDP-mannose | Reactome | 1 / 3 | 445× | 2.25e-3 | 2.48e-2 ✓ sig. |
| SUMOylation of DNA methylation proteins | Reactome | 1 / 4 | 334× | 2.99e-3 | 3.07e-2 ✓ sig. |
| Type I hemidesmosome assembly | Reactome | 1 / 11 | 121× | 8.22e-3 | 6.07e-2 |
| Purine salvage | Reactome | 1 / 13 | 103× | 9.70e-3 | 6.74e-2 |
| KSRP (KHSRP) binds and destabilizes mRNA | Reactome | 1 / 15 | 89.0× | 1.12e-2 | 7.34e-2 |
| mRNA decay by 3' to 5' exoribonuclease | Reactome | 1 / 16 | 83.4× | 1.19e-2 | 7.61e-2 |
| Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA | Reactome | 1 / 17 | 78.5× | 1.27e-2 | 7.87e-2 |
| Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA | Reactome | 1 / 17 | 78.5× | 1.27e-2 | 7.87e-2 |
| ATF4 activates genes in response to endoplasmic reticulum stress | Reactome | 1 / 18 | 74.1× | 1.34e-2 | 8.14e-2 |
| Fructose and mannose metabolism | KEGG | 1 / 34 | 39.2× | 2.52e-2 | 1.17e-1 |
| Biosynthesis of nucleotide sugars | KEGG | 1 / 37 | 36.1× | 2.74e-2 | 1.23e-1 |
| Amino sugar and nucleotide sugar metabolism | KEGG | 1 / 38 | 35.1× | 2.81e-2 | 1.24e-1 |
| Phase 0 - rapid depolarisation | Reactome | 1 / 44 | 30.3× | 3.25e-2 | 1.35e-1 |
| Assembly of collagen fibrils and other multimeric structures | Reactome | 1 / 51 | 26.2× | 3.76e-2 | 1.46e-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 ⇵ |
|---|---|---|---|---|---|
| cell motility | GO:0048870 | 2 / 48 | 86.5× | 2.30e-4 | 5.57e-3 ✓ sig. |
| reflex | GO:0060004 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| small intestine smooth muscle contraction | GO:1990770 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| negative regulation of growth rate | GO:0045967 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| guanosine metabolic process | GO:0008617 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| dGTP metabolic process | GO:0046070 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| purine deoxyribonucleoside metabolic process | GO:0046122 | 1 / 1 | 2,076× | 4.82e-4 | 9.31e-3 ✓ sig. |
| response to wounding | GO:0009611 | 2 / 81 | 51.3× | 6.55e-4 | 1.14e-2 ✓ sig. |
| chromosomal DNA methylation maintenance following DNA replication | GO:0141119 | 1 / 2 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching | GO:1905931 | 1 / 2 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| thermosensory behavior | GO:0040040 | 1 / 2 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| behavioral response to acetic acid induced pain | GO:0061367 | 1 / 2 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| GDP-D-mannose biosynthetic process from fructose-6-phosphate | GO:0061729 | 1 / 2 | 1,038× | 9.63e-4 | 1.47e-2 ✓ sig. |
| dAMP salvage | GO:0106383 | 1 / 3 | 692× | 1.44e-3 | 1.87e-2 ✓ sig. |
| GDP-mannose biosynthetic process from mannose | GO:0061728 | 1 / 3 | 692× | 1.44e-3 | 1.87e-2 ✓ sig. |