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 345
6
Diseases
10
Unique genes
0.245
Avg. similarity score
Cerebellar diseases
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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Cerebellar diseases
Bone marrow diseases
Revesz debuse syndrome
Revesz syndrome
dyskeratosis congenita, autosomal dominant 3
Mowat-wilson syndrome
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Cerebellar diseases | 5 | 5 | 7 |
| Bone marrow diseases | 4 | 4 | 4 |
| Revesz debuse syndrome | 4 | 4 | 1 |
| Revesz syndrome | 4 | 4 | 1 |
| dyskeratosis congenita, autosomal dominant 3 | 4 | 4 | 1 |
| Mowat-wilson syndrome | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TINF2 | 5 / 6 | Bone marrow diseases, Cerebellar diseases, dyskeratosis congenita, autosomal dominant 3, Revesz debuse syndrome and 1 more |
| ZEB2 | 2 / 6 | Cerebellar diseases, Mowat-wilson syndrome |
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 ⇵ |
|---|---|---|---|---|---|
| Nitric oxide stimulates guanylate cyclase | Reactome | 1 / 3 | 400× | 2.50e-3 | 2.69e-2 ✓ sig. |
| Anchoring of the basal body to the plasma membrane | Reactome | 2 / 98 | 24.5× | 2.84e-3 | 2.96e-2 ✓ sig. |
| Telomere Extension By Telomerase | Reactome | 1 / 16 | 75.1× | 1.32e-2 | 8.07e-2 |
| Phase I - Functionalization of compounds | Reactome | 1 / 21 | 57.2× | 1.74e-2 | 9.50e-2 |
| Arginine biosynthesis | KEGG | 1 / 23 | 52.2× | 1.90e-2 | 9.98e-2 |
| Dopamine Neurotransmitter Release Cycle | Reactome | 1 / 23 | 52.2× | 1.90e-2 | 9.98e-2 |
| Glutathione conjugation | Reactome | 1 / 24 | 50.0× | 1.98e-2 | 1.02e-1 |
| Neurexins and neuroligins | Reactome | 1 / 32 | 37.5× | 2.63e-2 | 1.20e-1 |
| ROS and RNS production in phagocytes | Reactome | 1 / 34 | 35.3× | 2.80e-2 | 1.24e-1 |
| Detoxification of Reactive Oxygen Species | Reactome | 1 / 34 | 35.3× | 2.80e-2 | 1.24e-1 |
| ABC transporters | KEGG | 1 / 45 | 26.7× | 3.69e-2 | 1.45e-1 |
| Arginine and proline metabolism | KEGG | 1 / 50 | 24.0× | 4.09e-2 | 1.53e-1 |
| Packaging Of Telomere Ends | Reactome | 1 / 52 | 23.1× | 4.25e-2 | 1.57e-1 |
| Ion homeostasis | Reactome | 1 / 54 | 22.2× | 4.41e-2 | 1.60e-1 |
| Recognition and association of DNA glycosylase with site containing an affected purine | Reactome | 1 / 56 | 21.4× | 4.57e-2 | 1.63e-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 ⇵ |
|---|---|---|---|---|---|
| hindbrain development | GO:0030902 | 2 / 20 | 187× | 4.87e-5 | 1.76e-3 ✓ sig. |
| central nervous system development | GO:0007417 | 3 / 158 | 35.5× | 6.81e-5 | 2.27e-3 ✓ sig. |
| retina layer formation | GO:0010842 | 2 / 27 | 138× | 8.98e-5 | 2.79e-3 ✓ sig. |
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 5 / 1,208 | 7.7× | 2.14e-4 | 5.29e-3 ✓ sig. |
| cerebellum development | GO:0021549 | 2 / 55 | 68.0× | 3.77e-4 | 7.85e-3 ✓ sig. |
| nitric oxide storage | GO:0035732 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| synaptic signaling by nitric oxide | GO:0099163 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| positive regulation of sodium ion transmembrane transport | GO:1902307 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| positive regulation of polarized epithelial cell differentiation | GO:0030862 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| cloaca development | GO:0035844 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| pronephric nephron tubule morphogenesis | GO:0039008 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| quinone catabolic process | GO:1901662 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| regulation of telomere maintenance via telomere lengthening | GO:1904356 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| mammillary axonal complex development | GO:0061373 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
| positive regulation of myofibroblast contraction | GO:1904330 | 1 / 1 | 1,869× | 5.35e-4 | 9.98e-3 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| dyskeratosis congenita, autosomal dominant 3 | Revesz debuse syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| dyskeratosis congenita, autosomal dominant 3 | Revesz syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Revesz debuse syndrome | Revesz syndrome | 0.500 | 1 | 6.49e-5 | 2.34e-4 ✓ sig. |
| Bone marrow diseases | Revesz debuse syndrome | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Bone marrow diseases | Revesz syndrome | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Bone marrow diseases | dyskeratosis congenita, autosomal dominant 3 | 0.200 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Cerebellar diseases | Mowat-wilson syndrome | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Cerebellar diseases | Revesz debuse syndrome | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Cerebellar diseases | Revesz syndrome | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Cerebellar diseases | dyskeratosis congenita, autosomal dominant 3 | 0.125 | 1 | 4.55e-4 | 9.55e-4 ✓ sig. |
| Bone marrow diseases | Cerebellar diseases | 0.091 | 1 | 1.82e-3 | 2.66e-3 ✓ sig. |