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 83

12 diseases · 25 shared-gene connections
12 Diseases
10 Unique genes
0.299 Avg. similarity score
Ankylosis Most-connected disease (7 links)
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Disease Searched: Antley-bixler syndrome 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
Cardiofacial dysplasia 1 1 2
Congenital external auditory canal atresia 1 1 1
P450 oxidoreductase deficiency 1 1 1
craniosynostosis 4 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FGFR2 8 / 12 Ankylosis, Antley-bixler syndrome, Beare-stevenson cutis gyrata syndrome, Biliary tract neoplasms and 4 more
ERF 2 / 12 craniosynostosis 4, Crouzon syndrome
POR 2 / 12 Antley-bixler syndrome, P450 oxidoreductase deficiency
PRKACB 2 / 12 Biliary tract neoplasms, Cardiofacial dysplasia
TSHZ1 2 / 12 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 ⇵
CREB1 phosphorylation through the activation of Adenylate Cyclase
PRKACB, PRKACA
 Reactome 2 / 7 343× 1.31e-5 4.08e-4 ✓ sig.
HDL assembly
PRKACB, PRKACA
 Reactome 2 / 8 300× 1.74e-5 5.20e-4 ✓ sig.
Ras signaling pathway
FGFR2, PRKACB, PRKACA, FGFR1
 KEGG 4 / 237 20.3× 2.83e-5 7.78e-4 ✓ sig.
Calcium signaling pathway
FGFR2, PRKACB, PRKACA, FGFR1
 KEGG 4 / 254 18.9× 3.71e-5 9.72e-4 ✓ sig.
MAPK signaling pathway
FGFR2, PRKACB, PRKACA, FGFR1
 KEGG 4 / 299 16.1× 7.02e-5 1.64e-3 ✓ sig.
Rap1 signalling
PRKACB, PRKACA
 Reactome 2 / 16 150× 7.44e-5 1.71e-3 ✓ sig.
Regulation of insulin secretion
PRKACB, PRKACA
 Reactome 2 / 16 150× 7.44e-5 1.71e-3 ✓ sig.
PKA activation in glucagon signalling
PRKACB, PRKACA
 Reactome 2 / 17 141× 8.43e-5 1.90e-3 ✓ sig.
Parathyroid hormone synthesis, secretion and action
PRKACB, PRKACA, FGFR1
 KEGG 3 / 115 31.3× 9.77e-5 2.15e-3 ✓ sig.
DARPP-32 events
PRKACB, PRKACA
 Reactome 2 / 19 126× 1.06e-4 2.29e-3 ✓ sig.
PKA activation
PRKACB, PRKACA
 Reactome 2 / 19 126× 1.06e-4 2.29e-3 ✓ sig.
CD209 (DC-SIGN) signaling
PRKACB, PRKACA
 Reactome 2 / 21 114× 1.30e-4 2.69e-3 ✓ sig.
Oncogene Induced Senescence
ERF, MDM4
 Reactome 2 / 33 72.8× 3.25e-4 5.61e-3 ✓ sig.
FCGR3A-mediated IL10 synthesis
PRKACB, PRKACA
 Reactome 2 / 35 68.6× 3.66e-4 6.17e-3 ✓ sig.
Glucagon-like Peptide-1 (GLP1) regulates insulin secretion
PRKACB, PRKACA
 Reactome 2 / 36 66.7× 3.87e-4 6.46e-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 ⇵
fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development
FGFR2, FGFR1
 GO:0035607 2 / 2 1,869× 2.58e-7 2.68e-5 ✓ sig.
orbitofrontal cortex development
FGFR2, FGFR1
 GO:0021769 2 / 3 1,246× 7.73e-7 6.69e-5 ✓ sig.
ventricular zone neuroblast division
FGFR2, FGFR1
 GO:0021847 2 / 3 1,246× 7.73e-7 6.69e-5 ✓ sig.
positive regulation of phospholipase activity
FGFR2, FGFR1
 GO:0010518 2 / 4 934× 1.55e-6 1.19e-4 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress
PRKACB, PRKACA
 GO:0097700 2 / 9 415× 9.26e-6 4.96e-4 ✓ sig.
lung-associated mesenchyme development
FGFR2, FGFR1
 GO:0060484 2 / 9 415× 9.26e-6 4.96e-4 ✓ sig.
high-density lipoprotein particle assembly
PRKACB, PRKACA
 GO:0034380 2 / 10 374× 1.16e-5 5.88e-4 ✓ sig.
regulation of protein processing
PRKACB, PRKACA
 GO:0070613 2 / 11 340× 1.41e-5 6.90e-4 ✓ sig.
chordate embryonic development
FGFR2, FGFR1
 GO:0043009 2 / 11 340× 1.41e-5 6.90e-4 ✓ sig.
branching involved in salivary gland morphogenesis
FGFR2, FGFR1
 GO:0060445 2 / 12 311× 1.70e-5 7.93e-4 ✓ sig.
mesenchymal cell differentiation
FGFR2, FGFR1
 GO:0048762 2 / 13 287× 2.00e-5 9.06e-4 ✓ sig.
regulation of osteoblast differentiation
FGFR2, PRKACA
 GO:0045667 2 / 17 220× 3.49e-5 1.38e-3 ✓ sig.
renal water homeostasis
PRKACB, PRKACA
 GO:0003091 2 / 19 197× 4.39e-5 1.64e-3 ✓ sig.
middle ear morphogenesis
TSHZ1, FGFR1
 GO:0042474 2 / 22 170× 5.92e-5 2.05e-3 ✓ sig.
positive regulation of mesenchymal cell proliferation
FGFR2, FGFR1
 GO:0002053 2 / 26 144× 8.32e-5 2.65e-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 2.33e-4 ✓ sig.
Ankylosis Beare-stevenson cutis gyrata syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Cutis gyrata syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Ankylosis Congenital aural atresia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Ankylosis Crouzon syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Crouzon syndrome Cutis gyrata syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
craniosynostosis 4 Crouzon syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Congenital aural atresia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Crouzon syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital aural atresia Cutis gyrata syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital aural atresia Congenital external auditory canal atresia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cutis gyrata syndrome Pfeiffer syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Pfeiffer syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Ankylosis Pfeiffer syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Biliary tract neoplasms Cutis gyrata syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Beare-stevenson cutis gyrata syndrome Biliary tract neoplasms 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Ankylosis Biliary tract neoplasms 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Antley-bixler syndrome Cutis gyrata syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Antley-bixler syndrome Beare-stevenson cutis gyrata syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Antley-bixler syndrome P450 oxidoreductase deficiency 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Ankylosis Antley-bixler syndrome 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Biliary tract neoplasms Congenital aural atresia 0.200 1 3.90e-4 8.66e-4 ✓ sig.
Biliary tract neoplasms Crouzon syndrome 0.200 1 3.90e-4 8.66e-4 ✓ sig.
Biliary tract neoplasms Cardiofacial dysplasia 0.200 1 3.90e-4 8.66e-4 ✓ sig.
Antley-bixler syndrome Congenital aural atresia 0.200 1 3.90e-4 8.66e-4 ✓ sig.