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 510
6
Diseases
4
Unique genes
0.313
Avg. similarity score
Ritscher-schinzler syndrome
Most-connected disease (5 links)
Disease
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Ritscher-schinzler syndrome
Hereditary spastic paraplegia 8
Intellectual disability, congenital cardiac malformation and dandy-walker malformation
Ritscher-schinzel syndrome 1
Ritscher-schinzel syndrome 3
Ritscher-schinzel syndrome 4
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Ritscher-schinzler syndrome | 5 | 5 | 4 |
| Hereditary spastic paraplegia 8 | 3 | 3 | 1 |
| Intellectual disability, congenital cardiac malformation and dandy-walker malformation | 3 | 3 | 1 |
| Ritscher-schinzel syndrome 1 | 3 | 3 | 1 |
| Ritscher-schinzel syndrome 3 | 1 | 1 | 1 |
| Ritscher-schinzel syndrome 4 | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| WASHC5 | 4 / 6 | Hereditary spastic paraplegia 8, Intellectual disability, congenital cardiac malformation and dandy-walker malformation, Ritscher-schinzel syndrome 1, Ritscher-schinzler syndrome |
| DPYSL5 | 2 / 6 | Ritscher-schinzel syndrome 4, Ritscher-schinzler syndrome |
| VPS35L | 2 / 6 | Ritscher-schinzel syndrome 3, Ritscher-schinzler 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 ⇵ |
|---|---|---|---|---|---|
| CRMPs in Sema3A signaling | Reactome | 1 / 16 | 188× | 5.32e-3 | 3.80e-2 ✓ sig. |
| Axon guidance | KEGG | 1 / 183 | 16.4× | 5.96e-2 | 1.60e-1 |
| Neddylation | Reactome | 1 / 234 | 12.8× | 7.57e-2 | 1.84e-1 |
| Endocytosis | KEGG | 1 / 250 | 12.0× | 8.07e-2 | 1.91e-1 |
| Neutrophil degranulation | Reactome | 1 / 480 | 6.3× | 1.51e-1 | 2.76e-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 ⇵ |
|---|---|---|---|---|---|
| Golgi to plasma membrane transport | GO:0006893 | 2 / 33 | 283× | 1.81e-5 | 8.59e-4 ✓ sig. |
| endocytic recycling | GO:0032456 | 2 / 65 | 144× | 7.12e-5 | 2.40e-3 ✓ sig. |
| protein transport | GO:0015031 | 3 / 667 | 21.0× | 1.76e-4 | 4.64e-3 ✓ sig. |
| regulation of actin nucleation | GO:0051125 | 1 / 2 | 2,336× | 4.28e-4 | 8.53e-3 ✓ sig. |
| meiotic spindle assembly | GO:0090306 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| endosome fission | GO:0140285 | 1 / 3 | 1,557× | 6.42e-4 | 1.11e-2 ✓ sig. |
| polar body extrusion after meiotic divisions | GO:0040038 | 1 / 5 | 934× | 1.07e-3 | 1.51e-2 ✓ sig. |
| pyrimidine nucleobase catabolic process | GO:0006208 | 1 / 7 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| regulation of vesicle size | GO:0097494 | 1 / 7 | 667× | 1.50e-3 | 1.82e-2 ✓ sig. |
| protein-containing complex organization | GO:0043933 | 1 / 8 | 584× | 1.71e-3 | 1.96e-2 ✓ sig. |
| negative regulation of dendrite morphogenesis | GO:0050774 | 1 / 9 | 519× | 1.93e-3 | 2.07e-2 ✓ sig. |
| intracellular copper ion homeostasis | GO:0006878 | 1 / 18 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |
| regulation of Arp2/3 complex-mediated actin nucleation | GO:0034315 | 1 / 18 | 260× | 3.85e-3 | 2.94e-2 ✓ sig. |
| protein-containing complex localization | GO:0031503 | 1 / 20 | 234× | 4.27e-3 | 3.09e-2 ✓ sig. |
| oocyte maturation | GO:0001556 | 1 / 27 | 173× | 5.77e-3 | 3.56e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Hereditary spastic paraplegia 8 | Intellectual disability, congenital cardiac malformation and dandy-walker malformation | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Hereditary spastic paraplegia 8 | Ritscher-schinzel syndrome 1 | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Intellectual disability, congenital cardiac malformation and dandy-walker malformation | Ritscher-schinzel syndrome 1 | 0.500 | 1 | 6.46e-5 | 1.98e-4 ✓ sig. |
| Hereditary spastic paraplegia 8 | Ritscher-schinzler syndrome | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Intellectual disability, congenital cardiac malformation and dandy-walker malformation | Ritscher-schinzler syndrome | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Ritscher-schinzel syndrome 1 | Ritscher-schinzler syndrome | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Ritscher-schinzel syndrome 3 | Ritscher-schinzler syndrome | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |
| Ritscher-schinzel syndrome 4 | Ritscher-schinzler syndrome | 0.200 | 1 | 2.58e-4 | 5.38e-4 ✓ sig. |