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 506

6 diseases · 9 shared-gene connections
6 Diseases
8 Unique genes
0.275 Avg. similarity score
Familial ventricular tachycardia 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 ⇵
Familial ventricular tachycardia 4 4 2
Gingival diseases 4 4 7
Ventricular tachycardia 4 4 2
Hypertrichosis, congenital generalised, with gingival hyperplasia 3 3 1
Retractile testis 2 2 1
Hyaline fibromatosis 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ABCA5 4 / 6 Familial ventricular tachycardia, Gingival diseases, Hypertrichosis, congenital generalised, with gingival hyperplasia, Ventricular tachycardia
GNAI2 3 / 6 Familial ventricular tachycardia, Retractile testis, Ventricular tachycardia
ANTXR2 2 / 6 Gingival diseases, Hyaline fibromatosis
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 ⇵
Rap1 signaling pathway
GNAI2, FPR1, FGF7, PDGFB
 KEGG 4 / 211 28.5× 6.13e-6 1.95e-4 ✓ sig.
Renin secretion
GNAI2, KCNMA1
 KEGG 2 / 69 43.5× 8.91e-4 1.04e-2 ✓ sig.
Melanoma
FGF7, PDGFB
 KEGG 2 / 73 41.1× 9.97e-4 1.13e-2 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
FGF7, PDGFB
 Reactome 2 / 75 40.0× 1.05e-3 1.18e-2 ✓ sig.
Gap junction
GNAI2, PDGFB
 KEGG 2 / 89 33.7× 1.48e-3 1.52e-2 ✓ sig.
PIP3 activates AKT signaling
FGF7, PDGFB
 Reactome 2 / 93 32.3× 1.61e-3 1.62e-2 ✓ sig.
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
FGF7, PDGFB
 Reactome 2 / 103 29.2× 1.97e-3 1.89e-2 ✓ sig.
RAF/MAP kinase cascade
FGF7, PDGFB
 Reactome 2 / 124 24.2× 2.84e-3 2.45e-2 ✓ sig.
Pathways in cancer
GNAI2, FGF7, PDGFB
 KEGG 3 / 533 8.4× 4.12e-3 3.19e-2 ✓ sig.
cGMP-PKG signaling pathway
GNAI2, KCNMA1
 KEGG 2 / 166 18.1× 5.03e-3 3.66e-2 ✓ sig.
Formyl peptide receptors bind formyl peptides and many other ligands
FPR1
 Reactome 1 / 8 188× 5.32e-3 3.80e-2 ✓ sig.
Ca2+ activated K+ channels
KCNMA1
 Reactome 1 / 9 167× 5.98e-3 4.10e-2 ✓ sig.
FGFR2b ligand binding and activation
FGF7
 Reactome 1 / 10 150× 6.64e-3 4.39e-2 ✓ sig.
PLC beta mediated events
GNAI2
 Reactome 1 / 12 125× 7.97e-3 4.94e-2 ✓ sig.
Chemical carcinogenesis - receptor activation
GNAI2, FGF7
 KEGG 2 / 215 14.0× 8.32e-3 5.07e-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 ⇵
positive regulation of cell division
FGF7, PDGFB
 GO:0051781 2 / 48 97.3× 1.79e-4 4.70e-3 ✓ sig.
positive chemotaxis
FGF7, PDGFB
 GO:0050918 2 / 51 91.6× 2.02e-4 5.14e-3 ✓ sig.
positive regulation of vascular associated smooth muscle cell proliferation
GNAI2, PDGFB
 GO:1904707 2 / 53 88.1× 2.19e-4 5.40e-3 ✓ sig.
adenylate cyclase-modulating G protein-coupled receptor signaling pathway
GNAI2, FPR1
 GO:0007188 2 / 57 82.0× 2.53e-4 6.00e-3 ✓ sig.
positive regulation of endothelial cell proliferation
FGF7, PDGFB
 GO:0001938 2 / 69 67.7× 3.71e-4 7.80e-3 ✓ sig.
metanephric glomerular mesangial cell development
PDGFB
 GO:0072255 1 / 1 2,336× 4.28e-4 8.53e-3 ✓ sig.
positive regulation of metanephric mesenchymal cell migration
PDGFB
 GO:2000591 1 / 1 2,336× 4.28e-4 8.53e-3 ✓ sig.
response to wounding
FGF7, PDGFB
 GO:0009611 2 / 81 57.7× 5.11e-4 9.64e-3 ✓ sig.
cellular response to mycophenolic acid
PDGFB
 GO:0071506 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
positive regulation of reverse cholesterol transport
ABCA5
 GO:1903064 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
negative regulation of phosphatidylinositol biosynthetic process
PDGFB
 GO:0010512 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
positive regulation of TRAIL production
TNFRSF8
 GO:0032759 1 / 2 1,168× 8.56e-4 1.33e-2 ✓ sig.
positive regulation of cell population proliferation
GNAI2, FGF7, PDGFB
 GO:0008284 3 / 532 13.2× 1.15e-3 1.58e-2 ✓ sig.
positive regulation of glomerular filtration
PDGFB
 GO:0003104 1 / 3 779× 1.28e-3 1.67e-2 ✓ sig.
secretion by lung epithelial cell involved in lung growth
FGF7
 GO:0061033 1 / 3 779× 1.28e-3 1.67e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Familial ventricular tachycardia Ventricular tachycardia 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Familial ventricular tachycardia Retractile testis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial ventricular tachycardia Hypertrichosis, congenital generalised, with gingival hyperplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hypertrichosis, congenital generalised, with gingival hyperplasia Ventricular tachycardia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Retractile testis Ventricular tachycardia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Gingival diseases Hyaline fibromatosis 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Gingival diseases Hypertrichosis, congenital generalised, with gingival hyperplasia 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Familial ventricular tachycardia Gingival diseases 0.111 1 9.04e-4 1.41e-3 ✓ sig.
Gingival diseases Ventricular tachycardia 0.111 1 9.04e-4 1.41e-3 ✓ sig.