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 179

8 diseases · 13 shared-gene connections
8 Diseases
25 Unique genes
0.177 Avg. similarity score
Birdshot chorioretinopathy Most-connected disease (5 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Birdshot chorioretinopathy 5 5 5
Carbamazepine hypersensitivity 5 5 1
Thrombophlebitis 5 5 1
Aortic arch syndrome 4 4 6
Anti-nmda receptor encephalitis 2 2 4
Parapsoriasis 2 2 2
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 6 / 8 Anti-nmda receptor encephalitis, Aortic arch syndrome, Birdshot chorioretinopathy, Carbamazepine hypersensitivity and 2 more
HLA-A 3 / 8 Aortic arch syndrome, Birdshot chorioretinopathy, Parapsoriasis
TECPR2 2 / 8 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
HLA-B, HLA-A, LNPEP, HLA-E
 Reactome 4 / 8 240× 1.02e-9 1.14e-7 ✓ sig.
Allograft rejection
HLA-B, HLA-A, HLA-DRB1, IL2, HLA-E
 KEGG 5 / 39 61.6× 1.40e-8 1.17e-6 ✓ sig.
Type I diabetes mellitus
HLA-B, HLA-A, HLA-DRB1, IL2, HLA-E
 KEGG 5 / 44 54.6× 2.63e-8 2.05e-6 ✓ sig.
Graft-versus-host disease
HLA-B, HLA-A, HLA-DRB1, IL2, HLA-E
 KEGG 5 / 45 53.4× 2.95e-8 2.27e-6 ✓ sig.
Autoimmune thyroid disease
HLA-B, HLA-A, HLA-DRB1, IL2, HLA-E
 KEGG 5 / 54 44.5× 7.54e-8 5.10e-6 ✓ sig.
Antigen Presentation: Folding, assembly and peptide loading of class I MHC
HLA-B, HLA-A, ERAP2, HLA-E
 Reactome 4 / 25 76.9× 1.79e-7 1.09e-5 ✓ sig.
Human T-cell leukemia virus 1 infection
HLA-B, HLA-A, HLA-DRB1, IL2, HLA-E, SMAD3
 KEGG 6 / 224 12.9× 5.18e-6 1.96e-4 ✓ sig.
Viral myocarditis
HLA-B, HLA-A, HLA-DRB1, HLA-E
 KEGG 4 / 70 27.5× 1.22e-5 3.96e-4 ✓ sig.
Antigen processing and presentation
HLA-B, HLA-A, HLA-DRB1, HLA-E
 KEGG 4 / 81 23.7× 2.18e-5 6.41e-4 ✓ sig.
Interferon gamma signaling
HLA-B, HLA-A, HLA-DRB1, HLA-E
 Reactome 4 / 87 22.1× 2.89e-5 8.09e-4 ✓ sig.
ER-Phagosome pathway
HLA-B, HLA-A, HLA-E
 Reactome 3 / 30 48.0× 3.12e-5 8.62e-4 ✓ sig.
Herpes simplex virus 1 infection
HLA-B, IFIH1, HLA-A, HLA-DRB1, HLA-E
 KEGG 5 / 182 13.2× 3.14e-5 8.68e-4 ✓ sig.
Phagosome
HLA-B, HLA-A, HLA-DRB1, HLA-E
 KEGG 4 / 155 12.4× 2.73e-4 4.98e-3 ✓ sig.
Cellular senescence
HLA-B, HLA-A, HLA-E, SMAD3
 KEGG 4 / 157 12.2× 2.87e-4 5.18e-3 ✓ sig.
Cell adhesion molecules
HLA-B, HLA-A, HLA-DRB1, HLA-E
 KEGG 4 / 160 12.0× 3.09e-4 5.49e-3 ✓ 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 ⇵
antigen processing and presentation of peptide antigen via MHC class I
HLA-B, HLA-A, ERAP2, LNPEP, HLA-E
 GO:0002474 5 / 17 220× 1.71e-11 5.96e-9 ✓ sig.
protection from natural killer cell mediated cytotoxicity
HLA-B, HLA-A, HLA-E
 GO:0042270 3 / 6 374× 4.22e-8 5.86e-6 ✓ sig.
positive regulation of T cell mediated cytotoxicity
HLA-B, HLA-A, HLA-DRB1, HLA-E
 GO:0001916 4 / 34 87.9× 1.12e-7 1.33e-5 ✓ sig.
detection of bacterium
HLA-B, HLA-A, HLA-DRB1
 GO:0016045 3 / 12 187× 4.62e-7 4.37e-5 ✓ sig.
antigen processing and presentation
HLA-B, HLA-A, HLA-DRB1, HLA-E
 GO:0019882 4 / 48 62.3× 4.66e-7 4.40e-5 ✓ sig.
antigen processing and presentation of endogenous peptide antigen via MHC class Ib
HLA-B, HLA-A, HLA-E
 GO:0002476 3 / 14 160× 7.62e-7 6.67e-5 ✓ sig.
antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent
HLA-B, HLA-A, HLA-E
 GO:0002486 3 / 14 160× 7.62e-7 6.67e-5 ✓ sig.
positive regulation of CD8-positive, alpha-beta T cell activation
HLA-A, HLA-E
 GO:2001187 2 / 2 747× 1.72e-6 1.28e-4 ✓ sig.
positive regulation of CD8-positive, alpha-beta T cell proliferation
HLA-A, HLA-E
 GO:2000566 2 / 3 498× 5.15e-6 3.08e-4 ✓ sig.
CD8-positive, alpha-beta T cell activation
HLA-A, HLA-E
 GO:0036037 2 / 4 374× 1.03e-5 5.33e-4 ✓ sig.
adaptive immune response
HLA-B, HLA-A, HLA-DRB1, IL2, ERAP2, HLA-E
 GO:0002250 6 / 507 8.8× 4.42e-5 1.64e-3 ✓ sig.
antigen processing and presentation of endogenous peptide antigen via MHC class I
HLA-A, ERAP2
 GO:0019885 2 / 9 166× 6.15e-5 2.10e-3 ✓ sig.
immune response
HLA-B, HLA-A, HLA-DRB1, IL2, HLA-E, SMAD3
 GO:0006955 6 / 543 8.3× 6.47e-5 2.18e-3 ✓ sig.
immune system process
HLA-B, IFIH1, HLA-A, HLA-DRB1, IL2, ERAP2, HLA-E
 GO:0002376 7 / 943 5.5× 1.76e-4 4.61e-3 ✓ sig.
positive regulation of chondrocyte differentiation
SMAD3, SOX5
 GO:0032332 2 / 20 74.7× 3.22e-4 7.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Aortic arch syndrome Birdshot chorioretinopathy 0.200 2 1.26e-6 7.70e-6 ✓ sig.
Carbamazepine hypersensitivity Thrombophlebitis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Anti-nmda receptor encephalitis Carbamazepine hypersensitivity 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Anti-nmda receptor encephalitis Thrombophlebitis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Birdshot chorioretinopathy Carbamazepine hypersensitivity 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Birdshot chorioretinopathy Thrombophlebitis 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Birdshot chorioretinopathy Paraparesis 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Aortic arch syndrome Carbamazepine hypersensitivity 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Aortic arch syndrome Thrombophlebitis 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Birdshot chorioretinopathy Parapsoriasis 0.143 1 6.49e-4 1.22e-3 ✓ sig.
Aortic arch syndrome Parapsoriasis 0.125 1 7.79e-4 1.39e-3 ✓ sig.
Carbamazepine hypersensitivity Vertebral column disorder 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Thrombophlebitis Vertebral column disorder 0.071 1 8.44e-4 1.48e-3 ✓ sig.