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 316
6
Diseases
66
Unique genes
0.231
Avg. similarity score
Brachydactyly-short stature-retinits pigmentosa syndrome
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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Brachydactyly-short stature-retinits pigmentosa syndrome
Metaphyseal chondrodysplasia with retinitis pigmentosa
Retinitis pigmentosa with or without skeletal anomalies
metaphyseal chondrodysplasia-retinitis pigmentosa syndrome
Diverticulitis
Osteonecrosis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Brachydactyly-short stature-retinits pigmentosa syndrome | 5 | 5 | 1 |
| Metaphyseal chondrodysplasia with retinitis pigmentosa | 5 | 5 | 1 |
| Retinitis pigmentosa with or without skeletal anomalies | 5 | 5 | 1 |
| metaphyseal chondrodysplasia-retinitis pigmentosa syndrome | 5 | 5 | 1 |
| Diverticulitis | 4 | 4 | 28 |
| Osteonecrosis | 4 | 4 | 39 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CWC27 | 6 / 6 | Brachydactyly-short stature-retinits pigmentosa syndrome, Diverticulitis, Metaphyseal chondrodysplasia with retinitis pigmentosa, metaphyseal chondrodysplasia-retinitis pigmentosa syndrome and 2 more |
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 ⇵ |
|---|---|---|---|---|---|
| Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | KEGG | 2 / 21 | 17.3× | 5.84e-3 | 4.85e-2 ✓ sig. |
| Activation of Na-permeable kainate receptors | Reactome | 1 / 2 | 91.0× | 1.10e-2 | 7.25e-2 |
| ABO blood group biosynthesis | Reactome | 1 / 3 | 60.7× | 1.64e-2 | 9.17e-2 |
| Axon guidance | KEGG | 4 / 183 | 4.0× | 1.81e-2 | 9.75e-2 |
| Vasopressin regulates renal water homeostasis via Aquaporins | Reactome | 2 / 43 | 8.5× | 2.32e-2 | 1.12e-1 |
| Glutamatergic synapse | KEGG | 3 / 116 | 4.7× | 2.59e-2 | 1.19e-1 |
| Biosynthesis of maresin-like SPMs | Reactome | 1 / 6 | 30.3× | 3.25e-2 | 1.35e-1 |
| Vascular smooth muscle contraction | KEGG | 3 / 134 | 4.1× | 3.73e-2 | 1.46e-1 |
| RUNX3 regulates CDKN1A transcription | Reactome | 1 / 7 | 26.0× | 3.78e-2 | 1.47e-1 |
| G alpha (s) signalling events | Reactome | 3 / 140 | 3.9× | 4.17e-2 | 1.55e-1 |
| Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) | Reactome | 1 / 8 | 22.7× | 4.31e-2 | 1.58e-1 |
| G alpha (i) signalling events | Reactome | 4 / 249 | 2.9× | 4.79e-2 | 1.68e-1 |
| Ca2+ activated K+ channels | Reactome | 1 / 9 | 20.2× | 4.84e-2 | 1.68e-1 |
| Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) | Reactome | 1 / 9 | 20.2× | 4.84e-2 | 1.68e-1 |
| Post-translational modification: synthesis of GPI-anchored proteins | Reactome | 2 / 66 | 5.5× | 5.09e-2 | 1.73e-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 ⇵ |
|---|---|---|---|---|---|
| synaptic membrane adhesion | GO:0099560 | 4 / 29 | 39.1× | 3.15e-6 | 2.08e-4 ✓ sig. |
| modulation of chemical synaptic transmission | GO:0050804 | 5 / 121 | 11.7× | 6.83e-5 | 2.27e-3 ✓ sig. |
| chondroitin sulfate proteoglycan metabolic process | GO:0050654 | 2 / 6 | 94.4× | 1.83e-4 | 4.75e-3 ✓ sig. |
| dermatan sulfate proteoglycan biosynthetic process | GO:0050651 | 2 / 9 | 62.9× | 4.35e-4 | 8.68e-3 ✓ sig. |
| epoxygenase P450 pathway | GO:0019373 | 2 / 18 | 31.5× | 1.81e-3 | 2.15e-2 ✓ sig. |
| negative regulation of G protein-coupled receptor signaling pathway | GO:0045744 | 2 / 18 | 31.5× | 1.81e-3 | 2.15e-2 ✓ sig. |
| renal water homeostasis | GO:0003091 | 2 / 19 | 29.8× | 2.02e-3 | 2.28e-2 ✓ sig. |
| regulation of axonogenesis | GO:0050770 | 2 / 24 | 23.6× | 3.22e-3 | 2.92e-2 ✓ sig. |
| regulation of retina development in camera-type eye | GO:1902866 | 1 / 1 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| transition between slow and fast fiber | GO:0014886 | 1 / 1 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| cardiac endothelial to mesenchymal transition | GO:0140074 | 1 / 1 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| glucuronoside transport | GO:0015779 | 1 / 1 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| UDP-glucuronate metabolic process | GO:0046398 | 1 / 1 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| glycine import into mitochondrion | GO:1904983 | 1 / 1 | 283× | 3.53e-3 | 3.08e-2 ✓ sig. |
| endochondral ossification | GO:0001958 | 2 / 31 | 18.3× | 5.35e-3 | 3.80e-2 ✓ sig. |