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 267
7
Diseases
45
Unique genes
0.148
Avg. similarity score
Intellectual developmental disorder expressive speech dysmorphic
Most-connected disease (5 links)
Disease
Searched: Intellectual developmental disorder expressive speech dysmorphic
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Intellectual developmental disorder expressive speech dysmorphic
Schinzel-Giedion syndrome
Bundle branch block
Cerebral atrophy
Coronary aneurysm
Intellectual developmental disorder speech dysmorphic
Dock2 deficiency
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Intellectual developmental disorder expressive speech dysmorphic | 5 | 5 | 1 |
| Schinzel-Giedion syndrome | 5 | 5 | 1 |
| Bundle branch block | 4 | 4 | 4 |
| Cerebral atrophy | 3 | 3 | 7 |
| Coronary aneurysm | 3 | 3 | 32 |
| Intellectual developmental disorder speech dysmorphic | 3 | 3 | 5 |
| Dock2 deficiency | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SETBP1 | 6 / 7 | Bundle branch block, Cerebral atrophy, Coronary aneurysm, Intellectual developmental disorder expressive speech dysmorphic and 2 more |
| DOCK2 | 2 / 7 | Coronary aneurysm, Dock2 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 ⇵ |
|---|---|---|---|---|---|
| Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane | Reactome | 2 / 18 | 29.7× | 2.02e-3 | 2.30e-2 ✓ sig. |
| Defective MAN1B1 causes MRT15 | Reactome | 1 / 1 | 267× | 3.75e-3 | 3.58e-2 ✓ sig. |
| Defective PMM2 causes PMM2-CDG (CDG-1a) | Reactome | 1 / 1 | 267× | 3.75e-3 | 3.58e-2 ✓ sig. |
| Regulation of gap junction activity | Reactome | 1 / 3 | 89.0× | 1.12e-2 | 7.44e-2 |
| Synthesis of GDP-mannose | Reactome | 1 / 3 | 89.0× | 1.12e-2 | 7.44e-2 |
| SUMOylation of DNA methylation proteins | Reactome | 1 / 4 | 66.7× | 1.49e-2 | 8.82e-2 |
| Assembly and cell surface presentation of NMDA receptors | Reactome | 1 / 6 | 44.5× | 2.23e-2 | 1.12e-1 |
| Nef and signal transduction | Reactome | 1 / 8 | 33.4× | 2.96e-2 | 1.31e-1 |
| Ca2+ activated K+ channels | Reactome | 1 / 9 | 29.7× | 3.32e-2 | 1.40e-1 |
| RNA degradation | KEGG | 2 / 78 | 6.8× | 3.44e-2 | 1.42e-1 |
| Formation of annular gap junctions | Reactome | 1 / 11 | 24.3× | 4.05e-2 | 1.56e-1 |
| Gap junction | KEGG | 2 / 89 | 6.0× | 4.38e-2 | 1.63e-1 |
| Gap junction degradation | Reactome | 1 / 12 | 22.2× | 4.41e-2 | 1.63e-1 |
| Purine salvage | Reactome | 1 / 13 | 20.5× | 4.77e-2 | 1.71e-1 |
| mRNA decay by 5' to 3' exoribonuclease | Reactome | 1 / 14 | 19.1× | 5.12e-2 | 1.77e-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 ⇵ |
|---|---|---|---|---|---|
| cerebral cortex radially oriented cell migration | GO:0021799 | 2 / 13 | 63.9× | 4.35e-4 | 8.75e-3 ✓ sig. |
| prepulse inhibition | GO:0060134 | 2 / 14 | 59.3× | 5.07e-4 | 9.77e-3 ✓ sig. |
| nervous system development | GO:0007399 | 7 / 631 | 4.6× | 7.19e-4 | 1.23e-2 ✓ sig. |
| cochlea morphogenesis | GO:0090103 | 2 / 28 | 29.7× | 2.06e-3 | 2.33e-2 ✓ sig. |
| regulation of granulocyte chemotaxis | GO:0071622 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| regulation of systemic arterial blood pressure by baroreceptor feedback | GO:0003025 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| glossopharyngeal nerve development | GO:0021563 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| vagus nerve development | GO:0021564 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| microtubule-based transport | GO:0099111 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| protein alpha-1,2-demannosylation | GO:0036508 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| negative regulation of growth rate | GO:0045967 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| guanosine metabolic process | GO:0008617 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| dGTP metabolic process | GO:0046070 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| purine deoxyribonucleoside metabolic process | GO:0046122 | 1 / 1 | 415× | 2.41e-3 | 2.54e-2 ✓ sig. |
| brain development | GO:0007420 | 4 / 244 | 6.8× | 2.78e-3 | 2.76e-2 ✓ sig. |