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 236

9 diseases · 18 shared-gene connections
9 Diseases
14 Unique genes
0.261 Avg. similarity score
Cardiofacial dysplasia Most-connected disease (6 links)
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Disease Searched: Primary ciliary dyskinesia 14 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 ⇵
Cardiofacial dysplasia 6 6 2
Ellis-van creveld syndrome 6 6 9
Multiple congenital malformation syndrome 6 6 2
Cardioacrofacial dysplasia 1 4 4 1
Cardioacrofacial dysplasia 2 4 4 1
Male breast carcinoma 4 4 5
Primary pigmented nodular adrenocortical disease 4 4 4 1
Estrogen resistance 1 1 3
Primary ciliary dyskinesia 14 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PRKACA 5 / 9 Cardioacrofacial dysplasia 1, Cardiofacial dysplasia, Ellis-van creveld syndrome, Multiple congenital malformation syndrome and 1 more
PRKACB 5 / 9 Cardioacrofacial dysplasia 2, Cardiofacial dysplasia, Ellis-van creveld syndrome, Male breast carcinoma and 1 more
CCDC170 2 / 9 Estrogen resistance, Male breast carcinoma
CCDC39 2 / 9 Ellis-van creveld syndrome, Primary ciliary dyskinesia 14
ESR1 2 / 9 Estrogen resistance, Male breast carcinoma
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
PRKACA, PRKACB, EVC, EVC2, GLI1
 KEGG 5 / 56 76.6× 3.56e-9 2.94e-7 ✓ sig.
Hedgehog 'off' state
PRKACA, PRKACB, GLI1, WDR35
 Reactome 4 / 56 61.3× 4.10e-7 1.92e-5 ✓ sig.
Vasopressin-regulated water reabsorption
PRKACA, PRKACB, DYNC2LI1
 KEGG 3 / 44 58.5× 1.62e-5 4.37e-4 ✓ sig.
CREB1 phosphorylation through the activation of Adenylate Cyclase
PRKACA, PRKACB
 Reactome 2 / 7 245× 2.64e-5 6.54e-4 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption
PRKACA, PRKACB, ESR1
 KEGG 3 / 53 48.6× 2.85e-5 6.96e-4 ✓ sig.
Intraflagellar transport
DYNC2LI1, TRAF3IP1, WDR35
 Reactome 3 / 54 47.7× 3.02e-5 7.29e-4 ✓ sig.
HDL assembly
PRKACA, PRKACB
 Reactome 2 / 8 214× 3.52e-5 8.26e-4 ✓ sig.
Hedgehog 'on' state
EVC, EVC2, GLI1
 Reactome 3 / 70 36.8× 6.59e-5 1.36e-3 ✓ sig.
Rap1 signalling
PRKACA, PRKACB
 Reactome 2 / 16 107× 1.50e-4 2.62e-3 ✓ sig.
Regulation of insulin secretion
PRKACA, PRKACB
 Reactome 2 / 16 107× 1.50e-4 2.62e-3 ✓ sig.
PKA activation in glucagon signalling
PRKACA, PRKACB
 Reactome 2 / 17 101× 1.70e-4 2.89e-3 ✓ sig.
Endocrine resistance
PRKACA, PRKACB, ESR1
 KEGG 3 / 99 26.0× 1.85e-4 3.09e-3 ✓ sig.
Factors involved in megakaryocyte development and platelet production
PRKACA, PRKACB, RAD51B
 Reactome 3 / 99 26.0× 1.85e-4 3.09e-3 ✓ sig.
Activation of SMO
EVC, EVC2
 Reactome 2 / 18 95.3× 1.91e-4 3.16e-3 ✓ sig.
DARPP-32 events
PRKACA, PRKACB
 Reactome 2 / 19 90.3× 2.13e-4 3.45e-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 ⇵
negative regulation of smoothened signaling pathway
PRKACA, PRKACB, TRAF3IP1
 GO:0045879 3 / 35 114× 2.16e-6 1.61e-4 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress
PRKACA, PRKACB
 GO:0097700 2 / 9 297× 1.87e-5 8.78e-4 ✓ sig.
high-density lipoprotein particle assembly
PRKACA, PRKACB
 GO:0034380 2 / 10 267× 2.34e-5 1.04e-3 ✓ sig.
regulation of protein processing
PRKACA, PRKACB
 GO:0070613 2 / 11 243× 2.86e-5 1.20e-3 ✓ sig.
smoothened signaling pathway
EVC, EVC2, GLI1
 GO:0007224 3 / 94 42.6× 4.31e-5 1.65e-3 ✓ sig.
intraciliary retrograde transport
DYNC2LI1, WDR35
 GO:0035721 2 / 14 191× 4.72e-5 1.77e-3 ✓ sig.
regulation of osteoblast differentiation
PRKACA, GLI1
 GO:0045667 2 / 17 157× 7.04e-5 2.38e-3 ✓ sig.
renal water homeostasis
PRKACA, PRKACB
 GO:0003091 2 / 19 141× 8.85e-5 2.83e-3 ✓ sig.
intraciliary transport
TRAF3IP1, WDR35
 GO:0042073 2 / 36 74.2× 3.24e-4 7.08e-3 ✓ sig.
positive regulation of smoothened signaling pathway
EVC, GLI1
 GO:0045880 2 / 39 68.5× 3.80e-4 7.89e-3 ✓ sig.
protein localization to cilium
CCDC39, WDR35
 GO:0061512 2 / 44 60.7× 4.84e-4 9.28e-3 ✓ sig.
cell projection organization
DYNC2LI1, TRAF3IP1, WDR35
 GO:0030030 3 / 214 18.7× 4.91e-4 9.37e-3 ✓ sig.
cilium assembly
DYNC2LI1, TRAF3IP1, WDR35
 GO:0060271 3 / 237 16.9× 6.61e-4 1.14e-2 ✓ sig.
notochord regression
GLI1
 GO:0060032 1 / 1 1,335× 7.49e-4 1.23e-2 ✓ sig.
TORC1 signaling
PRKACA, PRKACB
 GO:0038202 2 / 67 39.8× 1.12e-3 1.55e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cardiofacial dysplasia Multiple congenital malformation syndrome 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Estrogen resistance Male breast carcinoma 0.286 2 2.50e-7 1.65e-6 ✓ sig.
Ellis-van creveld syndrome Multiple congenital malformation syndrome 0.200 2 3.00e-7 1.96e-6 ✓ sig.
Cardiofacial dysplasia Ellis-van creveld syndrome 0.200 2 3.00e-7 1.96e-6 ✓ sig.
Cardioacrofacial dysplasia 1 Primary pigmented nodular adrenocortical disease 4 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cardioacrofacial dysplasia 1 Cardiofacial dysplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Multiple congenital malformation syndrome Primary pigmented nodular adrenocortical disease 4 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cardiofacial dysplasia Primary pigmented nodular adrenocortical disease 4 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cardioacrofacial dysplasia 2 Multiple congenital malformation syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cardioacrofacial dysplasia 2 Cardiofacial dysplasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cardioacrofacial dysplasia 1 Multiple congenital malformation syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cardioacrofacial dysplasia 2 Male breast carcinoma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Cardioacrofacial dysplasia 2 Ellis-van creveld syndrome 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Cardioacrofacial dysplasia 1 Ellis-van creveld syndrome 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Ellis-van creveld syndrome Primary ciliary dyskinesia 14 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Ellis-van creveld syndrome Primary pigmented nodular adrenocortical disease 4 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Cardiofacial dysplasia Male breast carcinoma 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Male breast carcinoma Multiple congenital malformation syndrome 0.143 1 6.46e-4 1.09e-3 ✓ sig.