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 233

7 diseases · 12 shared-gene connections
7 Diseases
12 Unique genes
0.247 Avg. similarity score
Acrofacial dysostosis Most-connected disease (5 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 ⇵
Acrofacial dysostosis 5 5 4
Ellis-van creveld syndrome 5 5 9
Curry-hall syndrome 4 4 2
Weyers acrofacial dysostosis 4 4 3
acrofacial dysostosis, weyers type 4 4 1
SF3B4-related acrofacial dysostosis 1 1 1
primary ciliary dyskinesia 14 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
EVC2 5 / 7 Acrofacial dysostosis, acrofacial dysostosis, weyers type, Curry-hall syndrome, Ellis-van creveld syndrome and 1 more
EVC 4 / 7 Acrofacial dysostosis, Curry-hall syndrome, Ellis-van creveld syndrome, Weyers acrofacial dysostosis
CCDC39 2 / 7 Ellis-van creveld syndrome, primary ciliary dyskinesia 14
SF3B4 2 / 7 Acrofacial dysostosis, SF3B4-related acrofacial dysostosis
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 ⇵
Hedgehog signaling pathway
EVC, EVC2, GLI1, PRKACA, PRKACB
 KEGG 5 / 56 89.4× 1.42e-9 1.51e-7 ✓ sig.
Hedgehog 'off' state
GLI1, PRKACA, PRKACB, WDR35
 Reactome 4 / 56 71.5× 2.04e-7 1.22e-5 ✓ sig.
Vasopressin-regulated water reabsorption
DYNC2LI1, PRKACA, PRKACB
 KEGG 3 / 44 68.2× 9.86e-6 3.32e-4 ✓ sig.
Intraflagellar transport
DYNC2LI1, TRAF3IP1, WDR35
 Reactome 3 / 54 55.6× 1.84e-5 5.59e-4 ✓ sig.
CREB1 phosphorylation through the activation of Adenylate Cyclase
PRKACA, PRKACB
 Reactome 2 / 7 286× 1.92e-5 5.78e-4 ✓ sig.
HDL assembly
PRKACA, PRKACB
 Reactome 2 / 8 250× 2.55e-5 7.28e-4 ✓ sig.
Hedgehog 'on' state
EVC, EVC2, GLI1
 Reactome 3 / 70 42.9× 4.02e-5 1.07e-3 ✓ sig.
Rap1 signalling
PRKACA, PRKACB
 Reactome 2 / 16 125× 1.09e-4 2.41e-3 ✓ sig.
Regulation of insulin secretion
PRKACA, PRKACB
 Reactome 2 / 16 125× 1.09e-4 2.41e-3 ✓ sig.
Melanogenesis
PRKACA, PRKACB, CTNNB1
 KEGG 3 / 101 29.7× 1.20e-4 2.60e-3 ✓ sig.
PKA activation in glucagon signalling
PRKACA, PRKACB
 Reactome 2 / 17 118× 1.23e-4 2.66e-3 ✓ sig.
Activation of SMO
EVC, EVC2
 Reactome 2 / 18 111× 1.39e-4 2.92e-3 ✓ sig.
DARPP-32 events
PRKACA, PRKACB
 Reactome 2 / 19 105× 1.55e-4 3.19e-3 ✓ sig.
PKA activation
PRKACA, PRKACB
 Reactome 2 / 19 105× 1.55e-4 3.19e-3 ✓ sig.
CD209 (DC-SIGN) signaling
PRKACA, PRKACB
 Reactome 2 / 21 95.3× 1.90e-4 3.76e-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 ⇵
regulation of osteoblast differentiation
GLI1, PRKACA, CTNNB1
 GO:0045667 3 / 17 275× 1.37e-7 1.57e-5 ✓ sig.
negative regulation of smoothened signaling pathway
PRKACA, PRKACB, TRAF3IP1
 GO:0045879 3 / 35 133× 1.31e-6 1.03e-4 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress
PRKACA, PRKACB
 GO:0097700 2 / 9 346× 1.36e-5 6.62e-4 ✓ sig.
high-density lipoprotein particle assembly
PRKACA, PRKACB
 GO:0034380 2 / 10 311× 1.70e-5 7.89e-4 ✓ sig.
regulation of protein processing
PRKACA, PRKACB
 GO:0070613 2 / 11 283× 2.07e-5 9.23e-4 ✓ sig.
smoothened signaling pathway
EVC, EVC2, GLI1
 GO:0007224 3 / 94 49.7× 2.62e-5 1.10e-3 ✓ sig.
intraciliary retrograde transport
DYNC2LI1, WDR35
 GO:0035721 2 / 14 222× 3.43e-5 1.35e-3 ✓ sig.
lung development
GLI1, CCDC39, CTNNB1
 GO:0030324 3 / 108 43.3× 3.98e-5 1.51e-3 ✓ sig.
renal water homeostasis
PRKACA, PRKACB
 GO:0003091 2 / 19 164× 6.43e-5 2.17e-3 ✓ sig.
proximal/distal pattern formation
GLI1, CTNNB1
 GO:0009954 2 / 26 120× 1.22e-4 3.51e-3 ✓ sig.
embryonic heart tube development
TRAF3IP1, CTNNB1
 GO:0035050 2 / 26 120× 1.22e-4 3.51e-3 ✓ sig.
intraciliary transport
TRAF3IP1, WDR35
 GO:0042073 2 / 36 86.5× 2.35e-4 5.66e-3 ✓ sig.
positive regulation of smoothened signaling pathway
EVC, GLI1
 GO:0045880 2 / 39 79.9× 2.76e-4 6.33e-3 ✓ sig.
cell projection organization
DYNC2LI1, TRAF3IP1, WDR35
 GO:0030030 3 / 214 21.8× 3.02e-4 6.75e-3 ✓ sig.
protein localization to cilium
CCDC39, WDR35
 GO:0061512 2 / 44 70.8× 3.52e-4 7.48e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Curry-hall syndrome Weyers acrofacial dysostosis 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Acrofacial dysostosis Curry-hall syndrome 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Acrofacial dysostosis Weyers acrofacial dysostosis 0.333 2 1.52e-7 1.09e-6 ✓ sig.
Curry-hall syndrome Ellis-van creveld syndrome 0.200 2 3.04e-7 2.06e-6 ✓ sig.
Ellis-van creveld syndrome Weyers acrofacial dysostosis 0.182 2 9.11e-7 5.67e-6 ✓ sig.
Acrofacial dysostosis Ellis-van creveld syndrome 0.167 2 1.82e-6 1.08e-5 ✓ sig.
acrofacial dysostosis, weyers type Curry-hall syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
acrofacial dysostosis, weyers type Weyers acrofacial dysostosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Acrofacial dysostosis SF3B4-related acrofacial dysostosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Acrofacial dysostosis acrofacial dysostosis, weyers type 0.200 1 2.60e-4 6.40e-4 ✓ sig.
acrofacial dysostosis, weyers type Ellis-van creveld syndrome 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Ellis-van creveld syndrome primary ciliary dyskinesia 14 0.100 1 5.84e-4 1.14e-3 ✓ sig.