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 144
9
Diseases
52
Unique genes
0.128
Avg. similarity score
Complex cortical dysplasia with other brain malformations
Most-connected disease (7 links)
Disease
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Complex cortical dysplasia with other brain malformations
Cortical dysplasia with other brain malformations
Cortical development malformation
15q11.2 microdeletion syndrome
Congenital fibrosis of extraocular muscles
Tubulinopathy
complex cortical dysplasia with other brain malformations 2
lissencephaly spectrum disorders
goldberg-shprintzen syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Complex cortical dysplasia with other brain malformations | 7 | 7 | 8 |
| Cortical dysplasia with other brain malformations | 7 | 7 | 17 |
| Cortical development malformation | 6 | 6 | 27 |
| 15q11.2 microdeletion syndrome | 4 | 4 | 3 |
| Congenital fibrosis of extraocular muscles | 4 | 4 | 16 |
| Tubulinopathy | 3 | 3 | 4 |
| complex cortical dysplasia with other brain malformations 2 | 3 | 3 | 1 |
| lissencephaly spectrum disorders | 3 | 3 | 3 |
| goldberg-shprintzen syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TUBB2B | 5 / 9 | Complex cortical dysplasia with other brain malformations, Congenital fibrosis of extraocular muscles, Cortical development malformation, Cortical dysplasia with other brain malformations and 1 more |
| TUBG1 | 5 / 9 | 15q11.2 microdeletion syndrome, Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations and 1 more |
| KIF5C | 4 / 9 | Complex cortical dysplasia with other brain malformations, complex cortical dysplasia with other brain malformations 2, Cortical development malformation, Cortical dysplasia with other brain malformations |
| TUBB3 | 4 / 9 | Complex cortical dysplasia with other brain malformations, Congenital fibrosis of extraocular muscles, Cortical dysplasia with other brain malformations, Tubulinopathy |
| KIF2A | 3 / 9 | Complex cortical dysplasia with other brain malformations, Cortical development malformation, Cortical dysplasia with other brain malformations |
| TUBA1A | 3 / 9 | Congenital fibrosis of extraocular muscles, Cortical development malformation, Tubulinopathy |
| TUBB | 3 / 9 | Complex cortical dysplasia with other brain malformations, Congenital fibrosis of extraocular muscles, Cortical dysplasia with other brain malformations |
| TUBB2A | 3 / 9 | Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations, Tubulinopathy |
| APC2 | 2 / 9 | Cortical dysplasia with other brain malformations, lissencephaly spectrum disorders |
| DYNC1H1 | 2 / 9 | Cortical development malformation, Cortical dysplasia with other brain malformations |
| HRAS | 2 / 9 | Congenital fibrosis of extraocular muscles, Cortical development malformation |
| KIF26A | 2 / 9 | Complex cortical dysplasia with other brain malformations, Cortical dysplasia with other brain malformations |
| KIFBP | 2 / 9 | Cortical development malformation, goldberg-shprintzen syndrome |
| TUBGCP2 | 2 / 9 | Cortical development malformation, Cortical dysplasia with other brain malformations |
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 ⇵ |
|---|---|---|---|---|---|
| Motor proteins | KEGG | 13 / 194 | 15.5× | 1.25e-12 | 2.68e-10 ✓ sig. |
| Cilium Assembly | Reactome | 6 / 19 | 72.9× | 1.27e-10 | 1.79e-8 ✓ sig. |
| Kinesins | Reactome | 8 / 59 | 31.3× | 1.32e-10 | 1.86e-8 ✓ sig. |
| Recruitment of NuMA to mitotic centrosomes | Reactome | 9 / 94 | 22.1× | 2.08e-10 | 2.79e-8 ✓ sig. |
| Aggrephagy | Reactome | 7 / 40 | 40.4× | 3.13e-10 | 4.04e-8 ✓ sig. |
| RHO GTPases activate IQGAPs | Reactome | 6 / 32 | 43.3× | 4.07e-9 | 3.93e-7 ✓ sig. |
| Salmonella infection | KEGG | 11 / 248 | 10.2× | 6.67e-9 | 6.13e-7 ✓ sig. |
| COPI-dependent Golgi-to-ER retrograde traffic | Reactome | 8 / 99 | 18.7× | 8.93e-9 | 7.92e-7 ✓ sig. |
| Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane | Reactome | 5 / 18 | 64.2× | 1.03e-8 | 8.90e-7 ✓ sig. |
| MHC class II antigen presentation | Reactome | 8 / 123 | 15.0× | 4.97e-8 | 3.54e-6 ✓ sig. |
| Alzheimer disease | KEGG | 12 / 388 | 7.1× | 7.00e-8 | 4.80e-6 ✓ sig. |
| COPI-independent Golgi-to-ER retrograde traffic | Reactome | 6 / 51 | 27.2× | 7.60e-8 | 5.13e-6 ✓ sig. |
| Carboxyterminal post-translational modifications of tubulin | Reactome | 5 / 27 | 42.8× | 9.39e-8 | 6.20e-6 ✓ sig. |
| Gap junction | KEGG | 7 / 89 | 18.2× | 9.86e-8 | 6.46e-6 ✓ sig. |
| HSP90 chaperone cycle for steroid hormone receptors (SHR) | Reactome | 6 / 55 | 25.2× | 1.21e-7 | 7.72e-6 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| microtubule cytoskeleton organization | GO:0000226 | 13 / 149 | 31.4× | 1.50e-16 | 1.37e-13 ✓ sig. |
| microtubule-based process | GO:0007017 | 7 / 46 | 54.7× | 4.18e-11 | 1.31e-8 ✓ sig. |
| mitotic cell cycle | GO:0000278 | 9 / 142 | 22.8× | 1.82e-10 | 4.93e-8 ✓ sig. |
| neuron migration | GO:0001764 | 6 / 132 | 16.3× | 1.73e-6 | 1.28e-4 ✓ sig. |
| microtubule-based movement | GO:0007018 | 5 / 87 | 20.7× | 4.26e-6 | 2.64e-4 ✓ sig. |
| cerebral cortex development | GO:0021987 | 5 / 88 | 20.4× | 4.51e-6 | 2.76e-4 ✓ sig. |
| brain development | GO:0007420 | 7 / 244 | 10.3× | 4.82e-6 | 2.91e-4 ✓ sig. |
| cytoskeleton-dependent intracellular transport | GO:0030705 | 3 / 14 | 77.0× | 7.24e-6 | 4.03e-4 ✓ sig. |
| mitotic spindle organization | GO:0007052 | 4 / 58 | 24.8× | 2.02e-5 | 9.06e-4 ✓ sig. |
| insulin receptor signaling pathway | GO:0008286 | 4 / 80 | 18.0× | 7.21e-5 | 2.37e-3 ✓ sig. |
| neuron apoptotic process | GO:0051402 | 4 / 98 | 14.7× | 1.59e-4 | 4.28e-3 ✓ sig. |
| neurogenesis | GO:0022008 | 4 / 102 | 14.1× | 1.85e-4 | 4.79e-3 ✓ sig. |
| cytoplasmic microtubule organization | GO:0031122 | 3 / 46 | 23.4× | 2.84e-4 | 6.46e-3 ✓ sig. |
| nervous system development | GO:0007399 | 8 / 631 | 4.6× | 3.27e-4 | 7.13e-3 ✓ sig. |
| intracellular mRNA localization | GO:0008298 | 2 / 10 | 71.9× | 3.37e-4 | 7.27e-3 ✓ sig. |