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 402
5
Diseases
18
Unique genes
0.244
Avg. similarity score
Gross motor development delay
Most-connected disease (4 links)
Disease
Searched: COG4-congenital disorder of glycosylation
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COG4-congenital disorder of glycosylation
Gross motor development delay
Saul-wilson syndrome
microcephalic osteodysplastic dysplasia, Saul-Wilson type
Expressive language delay
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Gross motor development delay | 4 | 4 | 18 |
| COG4-congenital disorder of glycosylation | 3 | 3 | 1 |
| Saul-wilson syndrome | 3 | 3 | 1 |
| microcephalic osteodysplastic dysplasia, Saul-Wilson type | 3 | 3 | 1 |
| Expressive language delay | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| COG4 | 4 / 5 | COG4-congenital disorder of glycosylation, Gross motor development delay, microcephalic osteodysplastic dysplasia, Saul-Wilson type, Saul-wilson syndrome |
| KLF7 | 2 / 5 | Expressive language delay, Gross motor development delay |
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 ⇵ |
|---|---|---|---|---|---|
| Loss of MECP2 binding ability to 5hmC-DNA | Reactome | 1 / 1 | 667× | 1.50e-3 | 1.84e-2 ✓ sig. |
| Long-term depression | KEGG | 2 / 60 | 22.2× | 3.57e-3 | 3.46e-2 ✓ sig. |
| Loss of MECP2 binding ability to 5mC-DNA | Reactome | 1 / 3 | 222× | 4.49e-3 | 4.07e-2 ✓ sig. |
| MECP2 regulates neuronal receptors and channels | Reactome | 1 / 4 | 167× | 5.98e-3 | 4.93e-2 ✓ sig. |
| Calcium signaling pathway | KEGG | 3 / 254 | 7.9× | 6.03e-3 | 4.96e-2 ✓ sig. |
| Regulation of MECP2 expression and activity | Reactome | 1 / 6 | 111× | 8.96e-3 | 6.46e-2 |
| Hypertrophic cardiomyopathy | KEGG | 2 / 99 | 13.5× | 9.44e-3 | 6.69e-2 |
| COPI-mediated anterograde transport | Reactome | 2 / 101 | 13.2× | 9.81e-3 | 6.85e-2 |
| Thyroxine biosynthesis | Reactome | 1 / 7 | 95.3× | 1.04e-2 | 7.13e-2 |
| Dilated cardiomyopathy | KEGG | 2 / 105 | 12.7× | 1.06e-2 | 7.19e-2 |
| Platelet degranulation | Reactome | 2 / 123 | 10.8× | 1.43e-2 | 8.62e-2 |
| Transcriptional Regulation by MECP2 | Reactome | 1 / 10 | 66.7× | 1.49e-2 | 8.82e-2 |
| Presynaptic depolarization and calcium channel opening | Reactome | 1 / 12 | 55.6× | 1.78e-2 | 9.87e-2 |
| Spinocerebellar ataxia | KEGG | 2 / 144 | 9.3× | 1.93e-2 | 1.03e-1 |
| Regulation of insulin secretion | Reactome | 1 / 16 | 41.7× | 2.37e-2 | 1.16e-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 ⇵ |
|---|---|---|---|---|---|
| muscle contraction | GO:0006936 | 4 / 85 | 48.9× | 1.16e-6 | 9.40e-5 ✓ sig. |
| striated muscle contraction | GO:0006941 | 3 / 24 | 130× | 1.50e-6 | 1.16e-4 ✓ sig. |
| muscle filament sliding | GO:0030049 | 2 / 15 | 138× | 9.13e-5 | 2.83e-3 ✓ sig. |
| skeletal muscle contraction | GO:0003009 | 2 / 32 | 64.9× | 4.27e-4 | 8.64e-3 ✓ sig. |
| regulation of synaptic transmission, glutamatergic | GO:0051966 | 2 / 33 | 62.9× | 4.55e-4 | 9.05e-3 ✓ sig. |
| cardiac muscle contraction | GO:0060048 | 2 / 43 | 48.3× | 7.73e-4 | 1.29e-2 ✓ sig. |
| regulation of skeletal muscle contraction by action potential | GO:0100001 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| trans-synaptic signaling by BDNF | GO:0099191 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling | GO:0060683 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| regulation of glomerular mesangial cell proliferation | GO:0072124 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| regulation of peptidyl-serine phosphorylation | GO:0033135 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| regulation of RNA polymerase II regulatory region sequence-specific DNA binding | GO:1903025 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| lysophospholipid translocation | GO:0140329 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| regulation of phosphatidylethanolamine metabolic process | GO:0150175 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
| regulation of phosphatidylserine metabolic process | GO:0150178 | 1 / 1 | 1,038× | 9.63e-4 | 1.48e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| COG4-congenital disorder of glycosylation | Saul-wilson syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| COG4-congenital disorder of glycosylation | microcephalic osteodysplastic dysplasia, Saul-Wilson type | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| microcephalic osteodysplastic dysplasia, Saul-Wilson type | Saul-wilson syndrome | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| COG4-congenital disorder of glycosylation | Gross motor development delay | 0.053 | 1 | 1.17e-3 | 1.89e-3 ✓ sig. |
| Expressive language delay | Gross motor development delay | 0.053 | 1 | 1.17e-3 | 1.89e-3 ✓ sig. |
| Gross motor development delay | microcephalic osteodysplastic dysplasia, Saul-Wilson type | 0.053 | 1 | 1.17e-3 | 1.89e-3 ✓ sig. |
| Gross motor development delay | Saul-wilson syndrome | 0.053 | 1 | 1.17e-3 | 1.89e-3 ✓ sig. |