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 50

14 diseases · 27 shared-gene connections
14 Diseases
45 Unique genes
0.279 Avg. similarity score
Ankylosis Most-connected disease (7 links)
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Disease Searched: Biliary tract neoplasms 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 ⇵
Ankylosis 7 7 1
Beare-stevenson cutis gyrata syndrome 7 7 1
Cutis gyrata syndrome 7 7 1
Biliary tract neoplasms 6 6 3
Congenital aural atresia 6 6 2
Antley-bixler syndrome 5 5 3
Crouzon syndrome 5 5 2
Pfeiffer syndrome 3 3 3
Ocular hypotension 2 2 36
craniosynostosis 4 2 2 1
Cardiofacial dysplasia 1 1 2
Congenital external auditory canal atresia 1 1 1
Diabetic macular edema 1 1 1
P450 oxidoreductase deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FGFR2 8 / 14 Ankylosis, Antley-bixler syndrome, Beare-stevenson cutis gyrata syndrome, Biliary tract neoplasms and 4 more
ERF 3 / 14 craniosynostosis 4, Crouzon syndrome, Ocular hypotension
MRPL19 2 / 14 Diabetic macular edema, Ocular hypotension
POR 2 / 14 Antley-bixler syndrome, P450 oxidoreductase deficiency
PRKACB 2 / 14 Biliary tract neoplasms, Cardiofacial dysplasia
TSHZ1 2 / 14 Congenital aural atresia, Congenital external auditory canal atresia
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
FGFR2, ARAP3, PFN2, RASSF5, VEGFA, FGFR1
 KEGG 6 / 211 7.6× 1.26e-4 2.73e-3 ✓ sig.
Ras signaling pathway
FGFR2, PRKACB, PRKACA, RASSF5, VEGFA, FGFR1
 KEGG 6 / 237 6.8× 2.37e-4 4.51e-3 ✓ sig.
CREB1 phosphorylation through the activation of Adenylate Cyclase
PRKACB, PRKACA
 Reactome 2 / 7 76.3× 2.85e-4 5.22e-3 ✓ sig.
HDL assembly
PRKACB, PRKACA
 Reactome 2 / 8 66.7× 3.79e-4 6.55e-3 ✓ sig.
Pathways in cancer
FGFR2, PRKACB, PRKACA, DCC, GADD45G, RASSF5, VEGFA, FGFR1
 KEGG 8 / 533 4.0× 7.20e-4 1.08e-2 ✓ sig.
MAPK signaling pathway
FGFR2, PRKACB, PRKACA, GADD45G, VEGFA, FGFR1
 KEGG 6 / 299 5.4× 8.15e-4 1.19e-2 ✓ sig.
VEGFA-VEGFR2 Pathway
PRKACB, PRKACA, VEGFA
 Reactome 3 / 62 12.9× 1.59e-3 1.98e-2 ✓ sig.
Rap1 signalling
PRKACB, PRKACA
 Reactome 2 / 16 33.4× 1.59e-3 1.98e-2 ✓ sig.
Regulation of insulin secretion
PRKACB, PRKACA
 Reactome 2 / 16 33.4× 1.59e-3 1.98e-2 ✓ sig.
PKA activation in glucagon signalling
PRKACB, PRKACA
 Reactome 2 / 17 31.4× 1.80e-3 2.16e-2 ✓ sig.
DARPP-32 events
PRKACB, PRKACA
 Reactome 2 / 19 28.1× 2.25e-3 2.54e-2 ✓ sig.
PKA activation
PRKACB, PRKACA
 Reactome 2 / 19 28.1× 2.25e-3 2.54e-2 ✓ sig.
Calcium signaling pathway
FGFR2, PRKACB, PRKACA, VEGFA, FGFR1
 KEGG 5 / 254 5.3× 2.49e-3 2.74e-2 ✓ sig.
CD209 (DC-SIGN) signaling
PRKACB, PRKACA
 Reactome 2 / 21 25.4× 2.76e-3 2.95e-2 ✓ sig.
Signaling by FGFR1 amplification mutants
FGFR1
 Reactome 1 / 1 267× 3.75e-3 3.65e-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 ⇵
fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development
FGFR2, FGFR1
 GO:0035607 2 / 2 415× 5.67e-6 3.38e-4 ✓ sig.
orbitofrontal cortex development
FGFR2, FGFR1
 GO:0021769 2 / 3 277× 1.70e-5 8.01e-4 ✓ sig.
ventricular zone neuroblast division
FGFR2, FGFR1
 GO:0021847 2 / 3 277× 1.70e-5 8.01e-4 ✓ sig.
positive regulation of phospholipase activity
FGFR2, FGFR1
 GO:0010518 2 / 4 208× 3.39e-5 1.36e-3 ✓ sig.
bone trabecula morphogenesis
SEMA4D, VEGFA
 GO:0061430 2 / 4 208× 3.39e-5 1.36e-3 ✓ sig.
positive regulation of cold-induced thermogenesis
ESRRG, GADD45G, PRDM16, VEGFA
 GO:0120162 4 / 102 16.3× 1.05e-4 3.21e-3 ✓ sig.
positive regulation of axon extension involved in axon guidance
DSCAM, VEGFA
 GO:0048842 2 / 7 119× 1.18e-4 3.49e-3 ✓ sig.
lung-associated mesenchyme development
FGFR2, FGFR1
 GO:0060484 2 / 9 92.3× 2.02e-4 5.19e-3 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress
PRKACB, PRKACA
 GO:0097700 2 / 9 92.3× 2.02e-4 5.19e-3 ✓ sig.
high-density lipoprotein particle assembly
PRKACB, PRKACA
 GO:0034380 2 / 10 83.1× 2.52e-4 6.05e-3 ✓ sig.
regulation of protein processing
PRKACB, PRKACA
 GO:0070613 2 / 11 75.5× 3.08e-4 6.98e-3 ✓ sig.
chordate embryonic development
FGFR2, FGFR1
 GO:0043009 2 / 11 75.5× 3.08e-4 6.98e-3 ✓ sig.
branching involved in salivary gland morphogenesis
FGFR2, FGFR1
 GO:0060445 2 / 12 69.2× 3.69e-4 7.93e-3 ✓ sig.
ossification involved in bone maturation
ADAMTS7, SEMA4D
 GO:0043931 2 / 12 69.2× 3.69e-4 7.93e-3 ✓ sig.
mesenchymal cell differentiation
FGFR2, FGFR1
 GO:0048762 2 / 13 63.9× 4.35e-4 8.87e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Ankylosis Cutis gyrata syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Ankylosis Beare-stevenson cutis gyrata syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Cutis gyrata syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Ankylosis Congenital aural atresia 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Ankylosis Crouzon syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Crouzon syndrome Cutis gyrata syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
craniosynostosis 4 Crouzon syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Congenital aural atresia 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Crouzon syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Congenital aural atresia Cutis gyrata syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Congenital aural atresia Congenital external auditory canal atresia 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Cutis gyrata syndrome Pfeiffer syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Pfeiffer syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Ankylosis Pfeiffer syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Biliary tract neoplasms Cutis gyrata syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Biliary tract neoplasms 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Ankylosis Biliary tract neoplasms 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Antley-bixler syndrome Cutis gyrata syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Antley-bixler syndrome Beare-stevenson cutis gyrata syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Antley-bixler syndrome P450 oxidoreductase deficiency 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Ankylosis Antley-bixler syndrome 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Biliary tract neoplasms Congenital aural atresia 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Biliary tract neoplasms Crouzon syndrome 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Biliary tract neoplasms Cardiofacial dysplasia 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Antley-bixler syndrome Congenital aural atresia 0.200 1 3.90e-4 8.64e-4 ✓ sig.
craniosynostosis 4 Ocular hypotension 0.027 1 2.34e-3 3.24e-3 ✓ sig.
Diabetic macular edema Ocular hypotension 0.027 1 2.34e-3 3.24e-3 ✓ sig.