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Cluster 609

5 diseases · 6 shared-gene connections

5 Diseases

5 Unique genes

0.303 Avg. similarity score

Cochlear diseases Most-connected disease (4 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.

Cochlear diseases Deafness, autosomal recessive 23 Navajo neurohepatopathy Pain insensitivity Usher syndrome, type1d/f digenic

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cochlear diseases	4	4	2
Deafness, autosomal recessive 23	2	2	1
Navajo neurohepatopathy	2	2	3
Pain insensitivity	2	2	2
Usher syndrome, type1d/f digenic	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MPV17	3 / 5	Cochlear diseases, Navajo neurohepatopathy, Pain insensitivity
PCDH15	3 / 5	Cochlear diseases, Deafness, autosomal recessive 23, Usher syndrome, type1d/f digenic

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 ⇵
Presynaptic depolarization and calcium channel opening CACNA2D1	Reactome	1 / 12	200×	4.99e-3	3.64e-2 ✓ sig.
Class B/2 (Secretin family receptors) UCN	Reactome	1 / 18	133×	7.47e-3	4.73e-2 ✓ sig.
Synthesis, secretion, and deacylation of Ghrelin UCN	Reactome	1 / 19	126×	7.89e-3	4.92e-2 ✓ sig.
Phase 2 - plateau phase CACNA2D1	Reactome	1 / 25	96.1×	1.04e-2	5.82e-2
Phase 0 - rapid depolarisation CACNA2D1	Reactome	1 / 44	54.6×	1.82e-2	8.12e-2
Peroxisomal protein import MPV17	Reactome	1 / 63	38.1×	2.60e-2	9.96e-2
Peroxisome MPV17	KEGG	1 / 83	28.9×	3.41e-2	1.16e-1
Arrhythmogenic right ventricular cardiomyopathy CACNA2D1	KEGG	1 / 86	27.9×	3.53e-2	1.19e-1
Cardiac muscle contraction CACNA2D1	KEGG	1 / 87	27.6×	3.57e-2	1.19e-1
Hypertrophic cardiomyopathy CACNA2D1	KEGG	1 / 99	24.3×	4.05e-2	1.28e-1
Dilated cardiomyopathy CACNA2D1	KEGG	1 / 105	22.9×	4.30e-2	1.33e-1
Adrenergic signaling in cardiomyocytes CACNA2D1	KEGG	1 / 154	15.6×	6.25e-2	1.64e-1
Oxytocin signaling pathway CACNA2D1	KEGG	1 / 154	15.6×	6.25e-2	1.64e-1
Hormone signaling UCN	KEGG	1 / 219	11.0×	8.79e-2	2.00e-1
Cytoskeleton in muscle cells TRIM54	KEGG	1 / 232	10.4×	9.29e-2	2.07e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
inner ear development MPV17, PCDH15	GO:0048839	2 / 54	138×	8.15e-5	2.66e-3 ✓ sig.
regulation of mitochondrial DNA metabolic process MPV17	GO:1901858	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
sensory perception of sound PCDH15, UCN	GO:0007605	2 / 162	46.1×	7.34e-4	1.23e-2 ✓ sig.
membrane depolarization during bundle of His cell action potential CACNA2D1	GO:0086048	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
calcium ion transmembrane transport via high voltage-gated calcium channel CACNA2D1	GO:0061577	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
regulation of membrane repolarization during action potential CACNA2D1	GO:0098903	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
negative regulation of feeding behavior UCN	GO:2000252	1 / 5	747×	1.34e-3	1.71e-2 ✓ sig.
equilibrioception PCDH15	GO:0050957	1 / 6	623×	1.60e-3	1.88e-2 ✓ sig.
positive regulation of corticotropin secretion UCN	GO:0051461	1 / 6	623×	1.60e-3	1.88e-2 ✓ sig.
positive regulation of behavioral fear response UCN	GO:2000987	1 / 7	534×	1.87e-3	2.05e-2 ✓ sig.
positive regulation of cardiac muscle contraction UCN	GO:0060452	1 / 9	415×	2.41e-3	2.32e-2 ✓ sig.
negative regulation of cell size UCN	GO:0045792	1 / 9	415×	2.41e-3	2.32e-2 ✓ sig.
drinking behavior UCN	GO:0042756	1 / 9	415×	2.41e-3	2.32e-2 ✓ sig.
glomerular basement membrane development MPV17	GO:0032836	1 / 10	374×	2.67e-3	2.46e-2 ✓ sig.
negative regulation of hormone secretion UCN	GO:0046888	1 / 10	374×	2.67e-3	2.46e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Deafness, autosomal recessive 23	Usher syndrome, type1d/f digenic	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cochlear diseases	Deafness, autosomal recessive 23	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cochlear diseases	Usher syndrome, type1d/f digenic	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cochlear diseases	Pain insensitivity	0.250	1	2.58e-4	5.38e-4 ✓ sig.
Cochlear diseases	Navajo neurohepatopathy	0.200	1	3.87e-4	7.33e-4 ✓ sig.
Navajo neurohepatopathy	Pain insensitivity	0.200	1	3.87e-4	7.33e-4 ✓ sig.

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