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 277
6
Diseases
20
Unique genes
0.193
Avg. similarity score
Carbamazepine hypersensitivity
Most-connected disease (4 links)
Disease
Searched: Birdshot chorioretinopathy
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Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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Birdshot chorioretinopathy
Carbamazepine hypersensitivity
Thrombophlebitis
Anti-nmda receptor encephalitis
Vertebral column disorder
Paraparesis
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Carbamazepine hypersensitivity | 4 | 4 | 1 |
| Thrombophlebitis | 4 | 4 | 1 |
| Birdshot chorioretinopathy | 3 | 3 | 5 |
| Anti-nmda receptor encephalitis | 2 | 2 | 4 |
| Vertebral column disorder | 2 | 2 | 13 |
| Paraparesis | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| HLA-B | 5 / 6 | Anti-nmda receptor encephalitis, Birdshot chorioretinopathy, Carbamazepine hypersensitivity, Thrombophlebitis and 1 more |
| TECPR2 | 2 / 6 | Birdshot chorioretinopathy, Paraparesis |
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 ⇵ |
|---|---|---|---|---|---|
| Endosomal/Vacuolar pathway | Reactome | 3 / 8 | 225× | 2.20e-7 | 1.38e-5 ✓ sig. |
| Antigen Presentation: Folding, assembly and peptide loading of class I MHC | Reactome | 3 / 25 | 72.1× | 8.87e-6 | 3.23e-4 ✓ sig. |
| ER-Phagosome pathway | Reactome | 2 / 30 | 40.0× | 1.11e-3 | 1.53e-2 ✓ sig. |
| Allograft rejection | KEGG | 2 / 39 | 30.8× | 1.88e-3 | 2.27e-2 ✓ sig. |
| Cellular senescence | KEGG | 3 / 157 | 11.5× | 2.12e-3 | 2.48e-2 ✓ sig. |
| Type I diabetes mellitus | KEGG | 2 / 44 | 27.3× | 2.39e-3 | 2.70e-2 ✓ sig. |
| Graft-versus-host disease | KEGG | 2 / 45 | 26.7× | 2.50e-3 | 2.78e-2 ✓ sig. |
| Herpes simplex virus 1 infection | KEGG | 3 / 182 | 9.9× | 3.23e-3 | 3.32e-2 ✓ sig. |
| Autoimmune thyroid disease | KEGG | 2 / 54 | 22.2× | 3.58e-3 | 3.58e-2 ✓ sig. |
| SMAD4 MH2 Domain Mutants in Cancer | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.51e-2 ✓ sig. |
| SMAD2/3 MH2 Domain Mutants in Cancer | Reactome | 1 / 3 | 200× | 4.99e-3 | 4.51e-2 ✓ sig. |
| Interferon alpha/beta signaling | Reactome | 2 / 67 | 17.9× | 5.46e-3 | 4.81e-2 ✓ sig. |
| Human T-cell leukemia virus 1 infection | KEGG | 3 / 224 | 8.0× | 5.77e-3 | 4.99e-2 ✓ sig. |
| Viral myocarditis | KEGG | 2 / 70 | 17.2× | 5.95e-3 | 5.10e-2 |
| Endocytosis | KEGG | 3 / 250 | 7.2× | 7.82e-3 | 6.06e-2 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| antigen processing and presentation of peptide antigen via MHC class I | GO:0002474 | 4 / 17 | 220× | 2.25e-9 | 4.61e-7 ✓ sig. |
| protection from natural killer cell mediated cytotoxicity | GO:0042270 | 2 / 6 | 311× | 1.63e-5 | 7.91e-4 ✓ sig. |
| antigen processing and presentation of endogenous peptide antigen via MHC class I | GO:0019885 | 2 / 9 | 208× | 3.90e-5 | 1.54e-3 ✓ sig. |
| detection of bacterium | GO:0016045 | 2 / 12 | 156× | 7.14e-5 | 2.43e-3 ✓ sig. |
| antigen processing and presentation of endogenous peptide antigen via MHC class Ib | GO:0002476 | 2 / 14 | 133× | 9.83e-5 | 3.10e-3 ✓ sig. |
| antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent | GO:0002486 | 2 / 14 | 133× | 9.83e-5 | 3.10e-3 ✓ sig. |
| positive regulation of chondrocyte differentiation | GO:0032332 | 2 / 20 | 93.4× | 2.04e-4 | 5.29e-3 ✓ sig. |
| positive regulation of T cell mediated cytotoxicity | GO:0001916 | 2 / 34 | 55.0× | 5.98e-4 | 1.11e-2 ✓ sig. |
| mercury ion transport | GO:0015694 | 1 / 1 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| leukocyte adhesion to arterial endothelial cell | GO:0061757 | 1 / 1 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| plasma membrane selenite transport | GO:0097080 | 1 / 1 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| mitochondrial manganese ion transmembrane transport | GO:1990540 | 1 / 1 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| negative regulation of lung blood pressure | GO:0061767 | 1 / 1 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent | GO:0002480 | 1 / 1 | 934× | 1.07e-3 | 1.63e-2 ✓ sig. |
| developmental process | GO:0032502 | 2 / 47 | 39.8× | 1.14e-3 | 1.70e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Carbamazepine hypersensitivity | Thrombophlebitis | 0.500 | 1 | 6.49e-5 | 2.33e-4 ✓ sig. |
| Anti-nmda receptor encephalitis | Carbamazepine hypersensitivity | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Anti-nmda receptor encephalitis | Thrombophlebitis | 0.200 | 1 | 2.60e-4 | 6.51e-4 ✓ sig. |
| Birdshot chorioretinopathy | Carbamazepine hypersensitivity | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Birdshot chorioretinopathy | Thrombophlebitis | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Birdshot chorioretinopathy | Paraparesis | 0.167 | 1 | 3.25e-4 | 7.71e-4 ✓ sig. |
| Carbamazepine hypersensitivity | Vertebral column disorder | 0.071 | 1 | 8.44e-4 | 1.50e-3 ✓ sig. |
| Thrombophlebitis | Vertebral column disorder | 0.071 | 1 | 8.44e-4 | 1.50e-3 ✓ sig. |