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 315
6
Diseases
8
Unique genes
0.272
Avg. similarity score
Boichis syndrome
Most-connected disease (5 links)
Disease
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Boichis syndrome
Senior-boichis syndrome
Cerebellar malformation
Coach syndrome
Rhyns syndrome
Chylomicron retention disease
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Boichis syndrome | 5 | 5 | 2 |
| Senior-boichis syndrome | 5 | 5 | 2 |
| Cerebellar malformation | 4 | 4 | 2 |
| Coach syndrome | 4 | 4 | 5 |
| Rhyns syndrome | 4 | 4 | 1 |
| Chylomicron retention disease | 2 | 2 | 2 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| TMEM67 | 5 / 6 | Boichis syndrome, Cerebellar malformation, Coach syndrome, Rhyns syndrome and 1 more |
| DCDC2 | 3 / 6 | Boichis syndrome, Chylomicron retention disease, Senior-boichis 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 ⇵ |
|---|---|---|---|---|---|
| Anchoring of the basal body to the plasma membrane | Reactome | 4 / 98 | 61.3× | 2.85e-7 | 1.63e-5 ✓ sig. |
| Hedgehog 'off' state | Reactome | 2 / 56 | 53.6× | 5.87e-4 | 9.03e-3 ✓ sig. |
| ARL13B-mediated ciliary trafficking of INPP5E | Reactome | 1 / 3 | 500× | 2.00e-3 | 2.28e-2 ✓ sig. |
| Chylomicron assembly | Reactome | 1 / 9 | 167× | 5.98e-3 | 4.92e-2 ✓ sig. |
| Synthesis of PIPs at the Golgi membrane | Reactome | 1 / 18 | 83.4× | 1.19e-2 | 7.61e-2 |
| Antigen Presentation: Folding, assembly and peptide loading of class I MHC | Reactome | 1 / 25 | 60.1× | 1.65e-2 | 9.23e-2 |
| Cargo concentration in the ER | Reactome | 1 / 33 | 45.5× | 2.18e-2 | 1.08e-1 |
| Legionellosis | KEGG | 1 / 56 | 26.8× | 3.67e-2 | 1.45e-1 |
| COPII-mediated vesicle transport | Reactome | 1 / 68 | 22.1× | 4.44e-2 | 1.60e-1 |
| Loss of Nlp from mitotic centrosomes | Reactome | 1 / 70 | 21.4× | 4.57e-2 | 1.63e-1 |
| Loss of proteins required for interphase microtubule organization from the centrosome | Reactome | 1 / 70 | 21.4× | 4.57e-2 | 1.63e-1 |
| Inositol phosphate metabolism | KEGG | 1 / 73 | 20.6× | 4.76e-2 | 1.67e-1 |
| AURKA Activation by TPX2 | Reactome | 1 / 73 | 20.6× | 4.76e-2 | 1.67e-1 |
| Recruitment of mitotic centrosome proteins and complexes | Reactome | 1 / 82 | 18.3× | 5.33e-2 | 1.78e-1 |
| Regulation of PLK1 Activity at G2/M Transition | Reactome | 1 / 88 | 17.1× | 5.72e-2 | 1.84e-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 ⇵ |
|---|---|---|---|---|---|
| cilium assembly | GO:0060271 | 6 / 237 | 59.1× | 1.07e-10 | 3.06e-8 ✓ sig. |
| cell projection organization | GO:0030030 | 4 / 214 | 43.7× | 1.13e-6 | 9.14e-5 ✓ sig. |
| axoneme assembly | GO:0035082 | 2 / 33 | 142× | 8.41e-5 | 2.66e-3 ✓ sig. |
| non-motile cilium assembly | GO:1905515 | 2 / 57 | 82.0× | 2.53e-4 | 5.97e-3 ✓ sig. |
| camera-type eye development | GO:0043010 | 2 / 74 | 63.1× | 4.27e-4 | 8.59e-3 ✓ sig. |
| determination of left/right symmetry | GO:0007368 | 2 / 83 | 56.3× | 5.36e-4 | 9.99e-3 ✓ sig. |
| lipid export from cell | GO:0140353 | 1 / 2 | 1,168× | 8.56e-4 | 1.36e-2 ✓ sig. |
| negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation | GO:2000314 | 1 / 2 | 1,168× | 8.56e-4 | 1.36e-2 ✓ sig. |
| negative regulation of protein localization to cilium | GO:1903565 | 1 / 3 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| kidney development | GO:0001822 | 2 / 146 | 32.0× | 1.65e-3 | 2.02e-2 ✓ sig. |
| response to inositol | GO:1902140 | 1 / 4 | 584× | 1.71e-3 | 2.07e-2 ✓ sig. |
| negative regulation of centrosome duplication | GO:0010826 | 1 / 5 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| regulation of lipid transport | GO:0032368 | 1 / 5 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| regulation of COPII vesicle coating | GO:0003400 | 1 / 5 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| protein localization to ciliary transition zone | GO:1904491 | 1 / 6 | 389× | 2.57e-3 | 2.58e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Boichis syndrome | Senior-boichis syndrome | 0.667 | 2 | 8.44e-9 | 7.20e-8 ✓ sig. |
| Boichis syndrome | Rhyns syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Cerebellar malformation | Rhyns syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Rhyns syndrome | Senior-boichis syndrome | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| Boichis syndrome | Cerebellar malformation | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Boichis syndrome | Chylomicron retention disease | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Cerebellar malformation | Senior-boichis syndrome | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Chylomicron retention disease | Senior-boichis syndrome | 0.250 | 1 | 2.60e-4 | 6.40e-4 ✓ sig. |
| Coach syndrome | Rhyns syndrome | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Boichis syndrome | Coach syndrome | 0.143 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Cerebellar malformation | Coach syndrome | 0.143 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| Coach syndrome | Senior-boichis syndrome | 0.143 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |