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 192

8 diseases · 13 shared-gene connections
8 Diseases
18 Unique genes
0.199 Avg. similarity score
Cinca syndrome Most-connected disease (5 links)
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Disease Searched: Cinca 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 ⇵
Cinca syndrome 5 5 1
Infantile neurological cutaneous and articular syndrome 5 5 1
Cold autoinflammatory syndrome 4 4 6
Cryopyrin-associated periodic syndrome 4 4 4
Autosomal dominant sensorineural deafness 3 3 6
Anaphylaxis 2 2 7
Autoinflammation, antibody deficiency, and immune dysregulation 2 2 1
Hearing loss with hypertrophic cardiomyopathy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
NLRP3 6 / 8 Anaphylaxis, Autosomal dominant sensorineural deafness, Cinca syndrome, Cold autoinflammatory syndrome and 2 more
PLCG2 3 / 8 Autoinflammation, antibody deficiency, and immune dysregulation, Cold autoinflammatory syndrome, Cryopyrin-associated periodic syndrome
MYO6 2 / 8 Autosomal dominant sensorineural deafness, Hearing loss with hypertrophic cardiomyopathy
NLRC4 2 / 8 Cold autoinflammatory syndrome, Cryopyrin-associated periodic syndrome
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 ⇵
Intrinsic Pathway of Fibrin Clot Formation
KNG1, F12
 Reactome 2 / 23 58.0× 5.27e-4 8.61e-3 ✓ sig.
G alpha (q) signalling events
KNG1, LTB4R, TRIO
 Reactome 3 / 172 11.6× 2.01e-3 2.37e-2 ✓ sig.
NOD-like receptor signaling pathway
NLRP3, NLRC4, NLRP12
 KEGG 3 / 187 10.7× 2.55e-3 2.82e-2 ✓ sig.
The IPAF inflammasome
NLRC4
 Reactome 1 / 2 334× 3.00e-3 3.15e-2 ✓ sig.
Pathogenic Escherichia coli infection
NLRP3, MYH9, MYO6
 KEGG 3 / 200 10.0× 3.09e-3 3.21e-2 ✓ sig.
Salmonella infection
NLRP3, NLRC4, MYO6
 KEGG 3 / 248 8.1× 5.64e-3 4.92e-2 ✓ sig.
Glioma
CAMK1D, PLCG2
 KEGG 2 / 76 17.6× 5.66e-3 4.92e-2 ✓ sig.
Shigellosis
NLRP3, PLCG2, NLRC4
 KEGG 3 / 250 8.0× 5.77e-3 4.99e-2 ✓ sig.
Leukotriene receptors
LTB4R
 Reactome 1 / 5 133× 7.47e-3 5.89e-2
Complement and coagulation cascades
KNG1, F12
 KEGG 2 / 88 15.2× 7.53e-3 5.91e-2
Fc gamma R-mediated phagocytosis
PLCG2, BIN1
 KEGG 2 / 98 13.6× 9.26e-3 6.77e-2
Inflammatory mediator regulation of TRP channels
KNG1, PLCG2
 KEGG 2 / 99 13.5× 9.44e-3 6.85e-2
C-type lectin receptor signaling pathway
NLRP3, PLCG2
 KEGG 2 / 105 12.7× 1.06e-2 7.35e-2
CD163 mediating an anti-inflammatory response
MYH9
 Reactome 1 / 9 74.1× 1.34e-2 8.46e-2
DCC mediated attractive signaling
TRIO
 Reactome 1 / 11 60.7× 1.64e-2 9.53e-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 interleukin-1 beta production
NLRP3, NLRC4, NLRP12
 GO:0032731 3 / 66 47.2× 3.31e-5 1.36e-3 ✓ sig.
inflammatory response
CAMK1D, KNG1, LTB4R, NLRP3, NLRC4
 GO:0006954 5 / 467 11.1× 6.24e-5 2.20e-3 ✓ sig.
actin filament-based movement
MYH9, MYO6
 GO:0030048 2 / 21 98.9× 1.82e-4 4.89e-3 ✓ sig.
pattern recognition receptor signaling pathway
NLRP3, NLRC4
 GO:0002221 2 / 21 98.9× 1.82e-4 4.89e-3 ✓ sig.
positive regulation of inflammatory response
NLRP3, NLRC4, NLRP12
 GO:0050729 3 / 122 25.5× 2.06e-4 5.33e-3 ✓ sig.
positive regulation of apoptotic process
CAMK1D, KNG1, NLRC4, BIN1
 GO:0043065 4 / 326 12.7× 2.29e-4 5.74e-3 ✓ sig.
positive regulation of NLRP3 inflammasome complex assembly
NLRP3, PLCG2
 GO:1900227 2 / 33 62.9× 4.55e-4 9.28e-3 ✓ sig.
regulation of canonical NF-kappaB signal transduction
PLCG2, NLRP12
 GO:0043122 2 / 36 57.7× 5.41e-4 1.04e-2 ✓ sig.
pyroptotic inflammatory response
NLRP3, NLRC4
 GO:0070269 2 / 40 51.9× 6.69e-4 1.20e-2 ✓ sig.
negative regulation of non-canonical NF-kappaB signal transduction
NLRP3, NLRP12
 GO:1901223 2 / 41 50.6× 7.03e-4 1.24e-2 ✓ sig.
negative regulation of ventricular cardiac muscle cell action potential
BIN1
 GO:1903946 1 / 1 1,038× 9.63e-4 1.52e-2 ✓ sig.
regulation of granulocyte chemotaxis
CAMK1D
 GO:0071622 1 / 1 1,038× 9.63e-4 1.52e-2 ✓ sig.
placenta development
MME, GJB3
 GO:0001890 2 / 48 43.3× 9.63e-4 1.52e-2 ✓ sig.
neuropeptide processing
MME
 GO:0061837 1 / 1 1,038× 9.63e-4 1.52e-2 ✓ sig.
regulation of interleukin-18 production
NLRP12
 GO:0032661 1 / 1 1,038× 9.63e-4 1.52e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cold autoinflammatory syndrome Cryopyrin-associated periodic syndrome 0.375 3 1.31e-10 1.29e-9 ✓ sig.
Cinca syndrome Infantile neurological cutaneous and articular syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Autoinflammation, antibody deficiency, and immune dysregulation Cryopyrin-associated periodic syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cinca syndrome Cryopyrin-associated periodic syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Cryopyrin-associated periodic syndrome Infantile neurological cutaneous and articular syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Autoinflammation, antibody deficiency, and immune dysregulation Cold autoinflammatory syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Autosomal dominant sensorineural deafness Infantile neurological cutaneous and articular syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Autosomal dominant sensorineural deafness Cinca syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Autosomal dominant sensorineural deafness Hearing loss with hypertrophic cardiomyopathy 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Cinca syndrome Cold autoinflammatory syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Cold autoinflammatory syndrome Infantile neurological cutaneous and articular syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Anaphylaxis Infantile neurological cutaneous and articular syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Anaphylaxis Cinca syndrome 0.125 1 4.55e-4 9.73e-4 ✓ sig.