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 333
6
Diseases
11
Unique genes
0.409
Avg. similarity score
Congenital neck anomaly
Most-connected disease (5 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Congenital neck anomaly
Distal nebulin myopathy
Nebulin-related myopathy
autosomal dominant nebulin-related myopathy
nemaline myopathy 2
Deglutition disorder
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Congenital neck anomaly | 5 | 5 | 2 |
| Distal nebulin myopathy | 4 | 4 | 1 |
| Nebulin-related myopathy | 4 | 4 | 1 |
| autosomal dominant nebulin-related myopathy | 4 | 4 | 1 |
| nemaline myopathy 2 | 4 | 4 | 1 |
| Deglutition disorder | 1 | 1 | 11 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| NEB | 6 / 6 | autosomal dominant nebulin-related myopathy, Congenital neck anomaly, Deglutition disorder, Distal nebulin myopathy and 2 more |
| RIF1 | 2 / 6 | Congenital neck anomaly, Deglutition disorder |
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 ⇵ |
|---|---|---|---|---|---|
| tRNA processing in the nucleus | Reactome | 3 / 57 | 57.5× | 1.63e-5 | 5.03e-4 ✓ sig. |
| Dopamine clearance from the synaptic cleft | Reactome | 1 / 1 | 1,092× | 9.16e-4 | 1.27e-2 ✓ sig. |
| Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) | Reactome | 1 / 1 | 1,092× | 9.16e-4 | 1.27e-2 ✓ sig. |
| SUMOylation of DNA methylation proteins | Reactome | 1 / 4 | 273× | 3.66e-3 | 3.54e-2 ✓ sig. |
| Formation of ATP by chemiosmotic coupling | Reactome | 1 / 18 | 60.7× | 1.64e-2 | 9.17e-2 |
| Cristae formation | Reactome | 1 / 18 | 60.7× | 1.64e-2 | 9.17e-2 |
| Na+/Cl- dependent neurotransmitter transporters | Reactome | 1 / 19 | 57.5× | 1.73e-2 | 9.50e-2 |
| Parkinson disease | KEGG | 2 / 268 | 8.1× | 2.39e-2 | 1.14e-1 |
| Striated Muscle Contraction | Reactome | 1 / 36 | 30.3× | 3.25e-2 | 1.35e-1 |
| Cocaine addiction | KEGG | 1 / 49 | 22.3× | 4.40e-2 | 1.60e-1 |
| Cysteine and methionine metabolism | KEGG | 1 / 52 | 21.0× | 4.66e-2 | 1.65e-1 |
| Amphetamine addiction | KEGG | 1 / 69 | 15.8× | 6.14e-2 | 1.91e-1 |
| Nonhomologous End-Joining (NHEJ) | Reactome | 1 / 69 | 15.8× | 6.14e-2 | 1.91e-1 |
| PRC2 methylates histones and DNA | Reactome | 1 / 73 | 15.0× | 6.49e-2 | 1.96e-1 |
| Pathways of neurodegeneration - multiple diseases | KEGG | 2 / 480 | 4.5× | 6.91e-2 | 2.03e-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 ⇵ |
|---|---|---|---|---|---|
| tRNA-type intron splice site recognition and cleavage | GO:0000379 | 3 / 3 | 1,699× | 1.52e-10 | 4.18e-8 ✓ sig. |
| tRNA splicing, via endonucleolytic cleavage and ligation | GO:0006388 | 3 / 13 | 392× | 4.33e-8 | 5.99e-6 ✓ sig. |
| tRNA processing | GO:0008033 | 3 / 107 | 47.6× | 2.91e-5 | 1.19e-3 ✓ sig. |
| muscle cell proliferation | GO:0033002 | 1 / 1 | 1,699× | 5.89e-4 | 1.07e-2 ✓ sig. |
| regulation of skeletal muscle tissue development | GO:0048641 | 1 / 2 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| chromosomal DNA methylation maintenance following DNA replication | GO:0141119 | 1 / 2 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching | GO:1905931 | 1 / 2 | 849× | 1.18e-3 | 1.66e-2 ✓ sig. |
| mRNA processing | GO:0006397 | 3 / 410 | 12.4× | 1.52e-3 | 1.93e-2 ✓ sig. |
| skeletal muscle satellite cell activation | GO:0014719 | 1 / 3 | 566× | 1.76e-3 | 2.11e-2 ✓ sig. |
| epigenetic programming of gene expression | GO:0043045 | 1 / 3 | 566× | 1.76e-3 | 2.11e-2 ✓ sig. |
| cardiac muscle thin filament assembly | GO:0071691 | 1 / 3 | 566× | 1.76e-3 | 2.11e-2 ✓ sig. |
| muscle organ development | GO:0007517 | 2 / 114 | 29.8× | 1.96e-3 | 2.23e-2 ✓ sig. |
| cellular response to bisphenol A | GO:1903926 | 1 / 4 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| myoblast development | GO:0048627 | 1 / 4 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |
| somatic muscle development | GO:0007525 | 1 / 4 | 425× | 2.35e-3 | 2.48e-2 ✓ sig. |