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 300

6 diseases · 9 shared-gene connections
6 Diseases
11 Unique genes
0.194 Avg. similarity score
Dermatitis herpetiformis Most-connected disease (4 links)
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Disease Searched: Extrinsic allergic alveolitis 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 ⇵
Dermatitis herpetiformis 4 4 3
Refractory anemia 4 4 1
Spinal cord compression 4 4 3
Pregnancy disorder 3 3 4
Extrinsic allergic alveolitis 2 2 4
cutis laxa, autosomal dominant 1 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
TNF 5 / 6 Dermatitis herpetiformis, Extrinsic allergic alveolitis, Pregnancy disorder, Refractory anemia and 1 more
ELN 2 / 6 cutis laxa, autosomal dominant 1, Dermatitis herpetiformis
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 ⇵
Herpes simplex virus 1 infection
TNF, CCL2, LTA, TAP1
 KEGG 4 / 182 24.0× 1.55e-5 5.10e-4 ✓ sig.
IL-17 signaling pathway
TNF, CCL2, MUC5B
 KEGG 3 / 94 34.8× 7.32e-5 1.81e-3 ✓ sig.
Viral protein interaction with cytokine and cytokine receptor
TNF, CCL2, LTA
 KEGG 3 / 100 32.8× 8.81e-5 2.10e-3 ✓ sig.
TNF signaling pathway
TNF, CCL2, LTA
 KEGG 3 / 119 27.5× 1.48e-4 3.15e-3 ✓ sig.
Fluid shear stress and atherosclerosis
TNF, CCL2, PLAT
 KEGG 3 / 141 23.2× 2.44e-4 4.68e-3 ✓ sig.
Type I diabetes mellitus
TNF, LTA
 KEGG 2 / 44 49.6× 7.07e-4 1.08e-2 ✓ sig.
Interleukin-10 signaling
TNF, CCL2
 Reactome 2 / 47 46.5× 8.06e-4 1.19e-2 ✓ sig.
Lipid and atherosclerosis
TNF, CCL2, SOD2
 KEGG 3 / 216 15.2× 8.51e-4 1.24e-2 ✓ sig.
Malaria
TNF, CCL2
 KEGG 2 / 50 43.7× 9.12e-4 1.30e-2 ✓ sig.
Human cytomegalovirus infection
TNF, CCL2, TAP1
 KEGG 3 / 226 14.5× 9.70e-4 1.37e-2 ✓ sig.
TNFR2 non-canonical NF-kB pathway
TNF, LTA
 Reactome 2 / 69 31.6× 1.73e-3 2.13e-2 ✓ sig.
Cytokine-cytokine receptor interaction
TNF, CCL2, LTA
 KEGG 3 / 298 11.0× 2.15e-3 2.50e-2 ✓ sig.
Antigen processing and presentation
TNF, TAP1
 KEGG 2 / 81 27.0× 2.38e-3 2.68e-2 ✓ sig.
Rheumatoid arthritis
TNF, CCL2
 KEGG 2 / 95 23.0× 3.25e-3 3.34e-2 ✓ sig.
Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
IGF2
 Reactome 1 / 4 273× 3.66e-3 3.64e-2 ✓ 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 ⇵
positive regulation of chronic inflammatory response to antigenic stimulus
TNF, LTA
 GO:0002876 2 / 2 1,699× 3.15e-7 3.27e-5 ✓ sig.
animal organ morphogenesis
TNF, CCL2, ELN, IGF2
 GO:0009887 4 / 130 52.3× 7.11e-7 6.41e-5 ✓ sig.
response to isolation stress
TNF, SOD2
 GO:0035900 2 / 4 849× 1.89e-6 1.42e-4 ✓ sig.
response to hypoxia
TNF, PLAT, LTA, SOD2
 GO:0001666 4 / 176 38.6× 2.38e-6 1.71e-4 ✓ sig.
positive regulation of humoral immune response mediated by circulating immunoglobulin
TNF, LTA
 GO:0002925 2 / 5 680× 3.15e-6 2.14e-4 ✓ sig.
humoral immune response
TNF, CCL2, LTA
 GO:0006959 3 / 58 87.9× 4.60e-6 2.89e-4 ✓ sig.
positive regulation of glial cell proliferation
TNF, LTA
 GO:0060252 2 / 22 154× 7.23e-5 2.46e-3 ✓ sig.
response to lipopolysaccharide
TNF, LTA, SOD2
 GO:0032496 3 / 161 31.7× 9.84e-5 3.10e-3 ✓ sig.
positive regulation of mitotic nuclear division
TNF, IGF2
 GO:0045840 2 / 29 117× 1.27e-4 3.72e-3 ✓ sig.
negative regulation of fibroblast proliferation
LTA, SOD2
 GO:0048147 2 / 35 97.1× 1.85e-4 4.95e-3 ✓ sig.
positive regulation of extrinsic apoptotic signaling pathway
TNF, LTA
 GO:2001238 2 / 38 89.4× 2.19e-4 5.54e-3 ✓ sig.
positive regulation of nitric oxide biosynthetic process
TNF, SOD2
 GO:0045429 2 / 42 80.9× 2.68e-4 6.41e-3 ✓ sig.
response to xenobiotic stimulus
TNF, LTA, SOD2
 GO:0009410 3 / 248 20.6× 3.52e-4 7.75e-3 ✓ sig.
vasodilation
TNF, SOD2
 GO:0042311 2 / 50 68.0× 3.80e-4 8.17e-3 ✓ sig.
response to activity
TNF, SOD2
 GO:0014823 2 / 52 65.3× 4.11e-4 8.66e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
cutis laxa, autosomal dominant 1 Dermatitis herpetiformis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Dermatitis herpetiformis Refractory anemia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Refractory anemia Spinal cord compression 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Extrinsic allergic alveolitis Refractory anemia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Pregnancy disorder Refractory anemia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Dermatitis herpetiformis Spinal cord compression 0.167 1 5.84e-4 1.16e-3 ✓ sig.
Dermatitis herpetiformis Pregnancy disorder 0.143 1 7.79e-4 1.41e-3 ✓ sig.
Extrinsic allergic alveolitis Spinal cord compression 0.143 1 7.79e-4 1.41e-3 ✓ sig.
Pregnancy disorder Spinal cord compression 0.143 1 7.79e-4 1.41e-3 ✓ sig.