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Cluster 396

5 diseases · 6 shared-gene connections

5 Diseases

7 Unique genes

0.270 Avg. similarity score

Cryopyrin-associated periodic syndrome Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Charcot-Marie-Tooth disease type 2T 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.

Charcot-Marie-Tooth disease type 2T Cryopyrin-associated periodic syndrome Autoinflammation, antibody deficiency, and immune dysregulation Cold autoinflammatory syndrome Congenital membranous nephropathy

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cryopyrin-associated periodic syndrome	4	4	4
Autoinflammation, antibody deficiency, and immune dysregulation	2	2	1
Charcot-Marie-Tooth disease type 2T	2	2	1
Cold autoinflammatory syndrome	2	2	6
Congenital membranous nephropathy	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MME	3 / 5	Charcot-Marie-Tooth disease type 2T, Congenital membranous nephropathy, Cryopyrin-associated periodic syndrome
PLCG2	3 / 5	Autoinflammation, antibody deficiency, and immune dysregulation, Cold autoinflammatory syndrome, Cryopyrin-associated periodic syndrome
NLRC4	2 / 5	Cold autoinflammatory syndrome, Cryopyrin-associated periodic syndrome
NLRP3	2 / 5	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 ⇵
NOD-like receptor signaling pathway NLRP3, NLRC4, NLRP12	KEGG	3 / 187	27.5×	1.24e-4	2.69e-3 ✓ sig.
Shigellosis PLCG2, NLRP3, NLRC4	KEGG	3 / 250	20.6×	2.93e-4	5.34e-3 ✓ sig.
The IPAF inflammasome NLRC4	Reactome	1 / 2	858×	1.17e-3	1.56e-2 ✓ sig.
C-type lectin receptor signaling pathway PLCG2, NLRP3	KEGG	2 / 105	32.7×	1.55e-3	1.93e-2 ✓ sig.
Yersinia infection NLRP3, NLRC4	KEGG	2 / 138	24.9×	2.65e-3	2.87e-2 ✓ sig.
TP53 Regulates Transcription of Caspase Activators and Caspases NLRC4	Reactome	1 / 12	143×	6.97e-3	5.57e-2
Coronavirus disease - COVID-19 PLCG2, NLRP3	KEGG	2 / 238	14.4×	7.69e-3	5.93e-2
Salmonella infection NLRP3, NLRC4	KEGG	2 / 248	13.8×	8.33e-3	6.24e-2
The NLRP3 inflammasome NLRP3	Reactome	1 / 15	114×	8.71e-3	6.44e-2
Metabolism of Angiotensinogen to Angiotensins MME	Reactome	1 / 17	101×	9.87e-3	6.95e-2
Toll Like Receptor 4 (TLR4) Cascade PLCG2	Reactome	1 / 19	90.3×	1.10e-2	7.44e-2
Role of phospholipids in phagocytosis PLCG2	Reactome	1 / 21	81.7×	1.22e-2	7.91e-2
Renin-angiotensin system MME	KEGG	1 / 23	74.6×	1.33e-2	8.34e-2
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers PLCG2	Reactome	1 / 23	74.6×	1.33e-2	8.34e-2
Intrinsic Pathway of Fibrin Clot Formation F12	Reactome	1 / 23	74.6×	1.33e-2	8.34e-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	121×	1.46e-6	1.14e-4 ✓ sig.
positive regulation of inflammatory response NLRP3, NLRC4, NLRP12	GO:0050729	3 / 122	65.6×	9.32e-6	5.04e-4 ✓ sig.
pattern recognition receptor signaling pathway NLRP3, NLRC4	GO:0002221	2 / 21	254×	2.52e-5	1.08e-3 ✓ sig.
positive regulation of NLRP3 inflammasome complex assembly PLCG2, NLRP3	GO:1900227	2 / 33	162×	6.32e-5	2.19e-3 ✓ sig.
regulation of canonical NF-kappaB signal transduction PLCG2, NLRP12	GO:0043122	2 / 36	148×	7.53e-5	2.51e-3 ✓ sig.
pyroptotic inflammatory response NLRP3, NLRC4	GO:0070269	2 / 40	133×	9.32e-5	2.94e-3 ✓ sig.
negative regulation of non-canonical NF-kappaB signal transduction NLRP3, NLRP12	GO:1901223	2 / 41	130×	9.79e-5	3.04e-3 ✓ sig.
cellular response to cytokine stimulus MME, NLRP12	GO:0071345	2 / 53	101×	1.64e-4	4.47e-3 ✓ sig.
positive regulation of non-canonical NF-kappaB signal transduction NLRP3, NLRP12	GO:1901224	2 / 66	80.9×	2.55e-4	6.10e-3 ✓ sig.
neuropeptide processing MME	GO:0061837	1 / 1	2,670×	3.75e-4	8.02e-3 ✓ sig.
regulation of interleukin-18 production NLRP12	GO:0032661	1 / 1	2,670×	3.75e-4	8.02e-3 ✓ sig.
positive regulation of NF-kappaB transcription factor activity NLRP3, NLRC4	GO:0051092	2 / 80	66.7×	3.75e-4	8.02e-3 ✓ sig.
protein processing MME, F12	GO:0016485	2 / 95	56.2×	5.28e-4	1.01e-2 ✓ sig.
regulation of inflammatory response NLRP3, NLRP12	GO:0050727	2 / 106	50.4×	6.57e-4	1.17e-2 ✓ sig.
creatinine metabolic process MME	GO:0046449	1 / 2	1,335×	7.49e-4	1.28e-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	1.30e-9 ✓ sig.
Charcot-Marie-Tooth disease type 2T	Congenital membranous nephropathy	0.500	1	6.49e-5	2.32e-4 ✓ sig.
Autoinflammation, antibody deficiency, and immune dysregulation	Cryopyrin-associated periodic syndrome	0.200	1	2.60e-4	6.48e-4 ✓ sig.
Charcot-Marie-Tooth disease type 2T	Cryopyrin-associated periodic syndrome	0.200	1	2.60e-4	6.48e-4 ✓ sig.
Congenital membranous nephropathy	Cryopyrin-associated periodic syndrome	0.200	1	2.60e-4	6.48e-4 ✓ sig.
Autoinflammation, antibody deficiency, and immune dysregulation	Cold autoinflammatory syndrome	0.143	1	3.90e-4	8.64e-4 ✓ sig.

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