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 438
6
Diseases
5
Unique genes
0.222
Avg. similarity score
Encephalocele
Most-connected disease (5 links)
Disease
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Encephalocele
Epileptic encephalopathy, early infantile, 18
Infantile encephalopathy with epilepsy and dysmorphic corpus callosum
Joubert syndrome 17
Meckel syndrome 1
Meckel syndrome 6
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Encephalocele | 5 | 5 | 5 |
| Epileptic encephalopathy, early infantile, 18 | 2 | 2 | 1 |
| Infantile encephalopathy with epilepsy and dysmorphic corpus callosum | 2 | 2 | 1 |
| Joubert syndrome 17 | 1 | 1 | 1 |
| Meckel syndrome 1 | 1 | 1 | 1 |
| Meckel syndrome 6 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| SZT2 | 3 / 6 | Encephalocele, Epileptic encephalopathy, early infantile, 18, Infantile encephalopathy with epilepsy and dysmorphic corpus callosum |
| CC2D2A | 2 / 6 | Encephalocele, Meckel syndrome 6 |
| CPLANE1 | 2 / 6 | Encephalocele, Joubert syndrome 17 |
| MKS1 | 2 / 6 | Encephalocele, Meckel syndrome 1 |
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 ⇵ |
|---|---|---|---|---|---|
| Anchoring of the basal body to the plasma membrane | Reactome | 3 / 98 | 73.5× | 5.21e-6 | 1.70e-4 ✓ sig. |
| Amino acids regulate mTORC1 | Reactome | 1 / 55 | 43.7× | 2.27e-2 | 9.20e-2 |
| Hedgehog 'off' state | Reactome | 1 / 56 | 42.9× | 2.31e-2 | 9.30e-2 |
| Loss of Nlp from mitotic centrosomes | Reactome | 1 / 70 | 34.3× | 2.88e-2 | 1.06e-1 |
| Loss of proteins required for interphase microtubule organization from the centrosome | Reactome | 1 / 70 | 34.3× | 2.88e-2 | 1.06e-1 |
| AURKA Activation by TPX2 | Reactome | 1 / 73 | 32.9× | 3.00e-2 | 1.08e-1 |
| Recruitment of mitotic centrosome proteins and complexes | Reactome | 1 / 82 | 29.3× | 3.37e-2 | 1.15e-1 |
| Regulation of PLK1 Activity at G2/M Transition | Reactome | 1 / 88 | 27.3× | 3.61e-2 | 1.20e-1 |
| Recruitment of NuMA to mitotic centrosomes | Reactome | 1 / 94 | 25.6× | 3.85e-2 | 1.25e-1 |
| Neutrophil degranulation | Reactome | 1 / 480 | 5.0× | 1.85e-1 | 3.15e-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 projection organization | GO:0030030 | 4 / 214 | 69.9× | 8.29e-8 | 1.09e-5 ✓ sig. |
| cilium assembly | GO:0060271 | 4 / 237 | 63.1× | 1.25e-7 | 1.53e-5 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 3 / 57 | 197× | 2.68e-7 | 2.88e-5 ✓ sig. |
| embryonic brain development | GO:1990403 | 2 / 20 | 374× | 1.09e-5 | 5.80e-4 ✓ sig. |
| motile cilium assembly | GO:0044458 | 2 / 28 | 267× | 2.16e-5 | 9.80e-4 ✓ sig. |
| camera-type eye development | GO:0043010 | 2 / 74 | 101× | 1.54e-4 | 4.21e-3 ✓ sig. |
| determination of left/right symmetry | GO:0007368 | 2 / 83 | 90.1× | 1.93e-4 | 4.97e-3 ✓ sig. |
| neural tube closure | GO:0001843 | 2 / 85 | 87.9× | 2.03e-4 | 5.14e-3 ✓ sig. |
| regulation of superoxide dismutase activity | GO:1901668 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| smoothened signaling pathway involved in regulation of secondary heart field cardioblast proliferation | GO:0003271 | 1 / 1 | 3,737× | 2.68e-4 | 6.25e-3 ✓ sig. |
| ciliary basal body-plasma membrane docking | GO:0097711 | 1 / 2 | 1,869× | 5.35e-4 | 9.88e-3 ✓ sig. |
| kidney development | GO:0001822 | 2 / 146 | 51.2× | 5.97e-4 | 1.07e-2 ✓ sig. |
| ciliary transition zone assembly | GO:1905349 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| common bile duct development | GO:0061009 | 1 / 3 | 1,246× | 8.03e-4 | 1.28e-2 ✓ sig. |
| regulation of Wnt signaling pathway, planar cell polarity pathway | GO:2000095 | 1 / 5 | 747× | 1.34e-3 | 1.71e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Epileptic encephalopathy, early infantile, 18 | Infantile encephalopathy with epilepsy and dysmorphic corpus callosum | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Encephalocele | Infantile encephalopathy with epilepsy and dysmorphic corpus callosum | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Encephalocele | Epileptic encephalopathy, early infantile, 18 | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Encephalocele | Joubert syndrome 17 | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Encephalocele | Meckel syndrome 6 | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |
| Encephalocele | Meckel syndrome 1 | 0.167 | 1 | 3.23e-4 | 6.41e-4 ✓ sig. |