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 334

6 diseases · 7 shared-gene connections
6 Diseases
28 Unique genes
0.145 Avg. similarity score
Gingival diseases Most-connected disease (4 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 ⇵
Gingival diseases 4 4 7
Embryonal carcinoma 3 3 2
Gingivitis 3 3 1
Hodgkin disease 2 2 17
Hyaline fibromatosis 1 1 1
Prostatic hyperplasia 1 1 7

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

Gene ⇵ Member diseases ⇵ Linked diseases
TNFRSF8 4 / 6 Embryonal carcinoma, Gingival diseases, Gingivitis, Hodgkin disease
ANTXR2 2 / 6 Gingival diseases, Hyaline fibromatosis
FGF7 2 / 6 Gingival diseases, Prostatic hyperplasia
PDGFB 2 / 6 Gingival diseases, Prostatic hyperplasia
TNFSF8 2 / 6 Embryonal carcinoma, Hodgkin disease
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 ⇵
Prostate cancer
PDGFB, GSTP1, MAPK1, NFKBIA, KLK3, SRD5A2, PDGFD
 KEGG 7 / 98 30.6× 2.00e-9 2.05e-7 ✓ sig.
NF-kappa B signaling pathway
CD40, CD40LG, CFLAR, ICAM1, NFKBIA
 KEGG 5 / 105 20.4× 3.89e-6 1.55e-4 ✓ sig.
Growth hormone receptor signaling
MAPK1, PTPN1, PRL
 Reactome 3 / 14 91.9× 4.06e-6 1.60e-4 ✓ sig.
Cytokine-cytokine receptor interaction
TNFRSF8, TNFSF8, CD40, CD40LG, CSF3, IFNA2, PRL
 KEGG 7 / 298 10.1× 4.08e-6 1.61e-4 ✓ sig.
Malaria
CD40, CD40LG, CSF3, ICAM1
 KEGG 4 / 50 34.3× 5.06e-6 1.92e-4 ✓ sig.
Lipid and atherosclerosis
CD40, CD40LG, ICAM1, IFNA2, MAPK1, NFKBIA
 KEGG 6 / 216 11.9× 8.54e-6 2.94e-4 ✓ sig.
PI3K-Akt signaling pathway
FGF7, PDGFB, CSF3, IFNA2, MAPK1, PRL, PDGFD
 KEGG 7 / 361 8.3× 1.44e-5 4.52e-4 ✓ sig.
Melanoma
FGF7, PDGFB, MAPK1, PDGFD
 KEGG 4 / 73 23.5× 2.30e-5 6.70e-4 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
PDGFB, ICAM1, IFNA2, MAPK1, NFKBIA
 KEGG 5 / 196 10.9× 7.97e-5 1.86e-3 ✓ sig.
Toll-like receptor signaling pathway
CD40, IFNA2, MAPK1, NFKBIA
 KEGG 4 / 109 15.7× 1.11e-4 2.44e-3 ✓ sig.
Rap1 signaling pathway
FPR1, FGF7, PDGFB, MAPK1, PDGFD
 KEGG 5 / 211 10.2× 1.13e-4 2.47e-3 ✓ sig.
Toxoplasmosis
CD40, CD40LG, MAPK1, NFKBIA
 KEGG 4 / 112 15.3× 1.23e-4 2.66e-3 ✓ sig.
TNF signaling pathway
CFLAR, ICAM1, MAPK1, NFKBIA
 KEGG 4 / 119 14.4× 1.56e-4 3.21e-3 ✓ sig.
Pathways in cancer
FGF7, PDGFB, GSTP1, IFNA2, MAPK1, NFKBIA, KLK3
 KEGG 7 / 533 5.6× 1.71e-4 3.45e-3 ✓ sig.
Interleukin-10 signaling
FPR1, CSF3, ICAM1
 Reactome 3 / 47 27.4× 1.72e-4 3.47e-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 ⇵
positive regulation of glomerular mesangial cell proliferation
PDGFB, CFLAR, PDGFD
 GO:0072126 3 / 6 334× 6.01e-8 7.91e-6 ✓ sig.
response to nutrient levels
CD40, GSTP1, PTPN1, PRL, SRD5A2
 GO:0031667 5 / 79 42.2× 1.08e-7 1.29e-5 ✓ sig.
inflammatory response
FPR1, CD40, CD40LG, GATA3, IFNA2, NFKBIA, REL
 GO:0006954 7 / 467 10.0× 4.37e-6 2.69e-4 ✓ sig.
cellular response to platelet-derived growth factor stimulus
PDGFB, PTPN1, PDGFD
 GO:0036120 3 / 26 77.0× 7.65e-6 4.23e-4 ✓ sig.
positive regulation of endothelial cell apoptotic process
CD40, CD40LG, PTPN1
 GO:2000353 3 / 29 69.0× 1.07e-5 5.50e-4 ✓ sig.
response to follicle-stimulating hormone
SRD5A2, SRD5A1
 GO:0032354 2 / 4 334× 1.30e-5 6.40e-4 ✓ sig.
cellular response to insulin stimulus
CFLAR, GSTP1, PTPN1, SRD5A1
 GO:0032869 4 / 102 26.2× 1.55e-5 7.38e-4 ✓ sig.
response to exogenous dsRNA
IFNA2, MAPK1, NFKBIA
 GO:0043330 3 / 34 58.9× 1.75e-5 8.06e-4 ✓ sig.
cellular response to tumor necrosis factor
CD40, GATA3, MAPK1, NFKBIA
 GO:0071356 4 / 107 24.9× 1.87e-5 8.50e-4 ✓ sig.
response to testosterone
CFLAR, SRD5A2, SRD5A1
 GO:0033574 3 / 36 55.6× 2.08e-5 9.26e-4 ✓ sig.
positive regulation of canonical NF-kappaB signal transduction
CD40, CD40LG, CFLAR, REL, PRL
 GO:0043123 5 / 232 14.4× 2.20e-5 9.66e-4 ✓ sig.
signaling
TNFSF8, FPR1, CD40LG
 GO:0023052 3 / 42 47.7× 3.33e-5 1.32e-3 ✓ sig.
female genitalia development
SRD5A2, SRD5A1
 GO:0030540 2 / 7 191× 4.53e-5 1.67e-3 ✓ sig.
positive regulation of cell division
FGF7, PDGFB, PDGFD
 GO:0051781 3 / 48 41.7× 4.98e-5 1.79e-3 ✓ sig.
cellular response to cytokine stimulus
CSF3, GATA3, NFKBIA
 GO:0071345 3 / 53 37.8× 6.71e-5 2.24e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Embryonal carcinoma Hodgkin disease 0.111 2 1.15e-6 7.04e-6 ✓ sig.
Gingival diseases Prostatic hyperplasia 0.154 2 3.72e-6 2.09e-5 ✓ sig.
Embryonal carcinoma Gingivitis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Gingival diseases Hyaline fibromatosis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Gingival diseases Gingivitis 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Embryonal carcinoma Gingival diseases 0.111 1 9.09e-4 1.56e-3 ✓ sig.
Gingivitis Hodgkin disease 0.056 1 1.10e-3 1.81e-3 ✓ sig.