Disease Clusters | GeDiPNet

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Cluster 407

5 diseases · 6 shared-gene connections

5 Diseases

12 Unique genes

0.196 Avg. similarity score

Autosomal dominant sensorineural deafness Most-connected disease (3 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Autosomal dominant sensorineural deafness Sebastian syndrome macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss Renal hypertension Hearing loss with hypertrophic cardiomyopathy

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Autosomal dominant sensorineural deafness	3	3	6
Sebastian syndrome	3	3	1
macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss	3	3	1
Renal hypertension	2	2	7
Hearing loss with hypertrophic cardiomyopathy	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MYH9	4 / 5	Autosomal dominant sensorineural deafness, macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss, Renal hypertension, Sebastian syndrome
MYO6	2 / 5	Autosomal dominant sensorineural deafness, Hearing loss with hypertrophic cardiomyopathy

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 ⇵
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) CYP2C8, CYP2J2	Reactome	2 / 8	250×	2.55e-5	7.28e-4 ✓ sig.
Lipid and atherosclerosis NLRP3, CYP2C8, CYP2J2, HSPA8	KEGG	4 / 216	18.5×	4.50e-5	1.17e-3 ✓ sig.
Xenobiotics CYP2C8, CYP2J2	Reactome	2 / 24	83.4×	2.50e-4	4.64e-3 ✓ sig.
Vascular smooth muscle contraction MYH9, AGT, NPPA	KEGG	3 / 134	22.4×	2.78e-4	5.05e-3 ✓ sig.
Linoleic acid metabolism CYP2C8, CYP2J2	KEGG	2 / 30	66.7×	3.92e-4	6.61e-3 ✓ sig.
Pathogenic Escherichia coli infection NLRP3, MYH9, MYO6	KEGG	3 / 200	15.0×	8.96e-4	1.25e-2 ✓ sig.
Arachidonic acid metabolism CYP2C8, CYP2J2	KEGG	2 / 63	31.8×	1.73e-3	2.05e-2 ✓ sig.
Renin secretion AGT, NPPA	KEGG	2 / 69	29.0×	2.07e-3	2.34e-2 ✓ sig.
Aldosterone synthesis and secretion AGT, NPPA	KEGG	2 / 98	20.4×	4.12e-3	3.86e-2 ✓ sig.
Serotonergic synapse CYP2C8, CYP2J2	KEGG	2 / 115	17.4×	5.63e-3	4.74e-2 ✓ sig.
Biosynthesis of maresin-like SPMs CYP2C8	Reactome	1 / 6	167×	5.98e-3	4.92e-2 ✓ sig.
Clathrin-mediated endocytosis BIN1, HSPA8	Reactome	2 / 130	15.4×	7.15e-3	5.54e-2
CD163 mediating an anti-inflammatory response MYH9	Reactome	1 / 9	111×	8.96e-3	6.42e-2
Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) CYP2C8	Reactome	1 / 9	111×	8.96e-3	6.42e-2
CYP2E1 reactions CYP2C8	Reactome	1 / 11	91.0×	1.09e-2	7.25e-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 ⇵
organic acid metabolic process CYP2C8, CYP2J2	GO:0006082	2 / 8	389×	1.06e-5	5.43e-4 ✓ sig.
epoxygenase P450 pathway CYP2C8, CYP2J2	GO:0019373	2 / 18	173×	5.75e-5	2.00e-3 ✓ sig.
actin filament-based movement MYH9, MYO6	GO:0030048	2 / 21	148×	7.88e-5	2.53e-3 ✓ sig.
blood vessel diameter maintenance AGT, NPPA	GO:0097746	2 / 37	84.2×	2.49e-4	5.90e-3 ✓ sig.
arachidonate metabolic process CYP2C8, CYP2J2	GO:0019369	2 / 41	76.0×	3.06e-4	6.81e-3 ✓ sig.
negative regulation of ventricular cardiac muscle cell action potential BIN1	GO:1903946	1 / 1	1,557×	6.42e-4	1.13e-2 ✓ sig.
negative regulation of collecting lymphatic vessel constriction NPPA	GO:1903815	1 / 1	1,557×	6.42e-4	1.13e-2 ✓ sig.
regulation of protein import HSPA8	GO:1904589	1 / 1	1,557×	6.42e-4	1.13e-2 ✓ sig.
chaperone-mediated autophagy translocation complex disassembly HSPA8	GO:1904764	1 / 1	1,557×	6.42e-4	1.13e-2 ✓ sig.
regulation of blood pressure AGT, NPPA	GO:0008217	2 / 83	37.5×	1.25e-3	1.73e-2 ✓ sig.
regulation of renal output by angiotensin AGT	GO:0002019	1 / 2	779×	1.28e-3	1.75e-2 ✓ sig.
regulation of blood volume by renin-angiotensin AGT	GO:0002016	1 / 2	779×	1.28e-3	1.75e-2 ✓ sig.
G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger AGT	GO:0007199	1 / 2	779×	1.28e-3	1.75e-2 ✓ sig.
positive regulation of membrane hyperpolarization AGT	GO:1902632	1 / 2	779×	1.28e-3	1.75e-2 ✓ sig.
lipid tube assembly BIN1	GO:0060988	1 / 2	779×	1.28e-3	1.75e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss	Sebastian syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Autosomal dominant sensorineural deafness	Hearing loss with hypertrophic cardiomyopathy	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Autosomal dominant sensorineural deafness	Sebastian syndrome	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Autosomal dominant sensorineural deafness	macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss	0.143	1	3.90e-4	8.52e-4 ✓ sig.
macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss	Renal hypertension	0.125	1	4.55e-4	9.55e-4 ✓ sig.
Renal hypertension	Sebastian syndrome	0.125	1	4.55e-4	9.55e-4 ✓ sig.

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