Disease Clusters | GeDiPNet

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Cluster 224

7 diseases · 13 shared-gene connections

7 Diseases

9 Unique genes

0.227 Avg. similarity score

22q13 monosomy syndrome Most-connected disease (5 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.

22q13 monosomy syndrome 22q13.3 deletion syndrome Urinary bladder diseases Hyperkalemia Ventricular outflow obstruction phelan-mcdermid syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
22q13 monosomy syndrome	5	5	2
22q13.3 deletion syndrome	5	5	4
Urinary bladder diseases	5	5	5
Hyperkalemia	4	4	2
Ventricular outflow obstruction	4	4	1
phelan-mcdermid syndrome	2	2	1
sorsby fundus dystrophy	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
INS	5 / 7	22q13 monosomy syndrome, 22q13.3 deletion syndrome, Hyperkalemia, Urinary bladder diseases and 1 more
SHANK3	3 / 7	22q13 monosomy syndrome, 22q13.3 deletion syndrome, phelan-mcdermid syndrome
TIMP3	2 / 7	sorsby fundus dystrophy, Urinary bladder diseases

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 ⇵
Ovarian steroidogenesis INS, CYP17A1	KEGG	2 / 52	51.3×	6.49e-4	9.77e-3 ✓ sig.
Defective CYP17A1 causes Adrenal hyperplasia 5 (AH5) CYP17A1	Reactome	1 / 1	1,334×	7.49e-4	1.09e-2 ✓ sig.
Prolactin signaling pathway INS, CYP17A1	KEGG	2 / 71	37.6×	1.21e-3	1.56e-2 ✓ sig.
Signaling by Insulin receptor INS	Reactome	1 / 2	667×	1.50e-3	1.85e-2 ✓ sig.
Insulin secretion INS, CHRM3	KEGG	2 / 86	31.0×	1.77e-3	2.08e-2 ✓ sig.
Muscarinic acetylcholine receptors CHRM3	Reactome	1 / 5	267×	3.74e-3	3.59e-2 ✓ sig.
IRS activation INS	Reactome	1 / 5	267×	3.74e-3	3.59e-2 ✓ sig.
Insulin receptor signalling cascade INS	Reactome	1 / 6	222×	4.49e-3	4.08e-2 ✓ sig.
Glucocorticoid biosynthesis CYP17A1	Reactome	1 / 10	133×	7.47e-3	5.69e-2
FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes INS	Reactome	1 / 10	133×	7.47e-3	5.69e-2
Signal attenuation INS	Reactome	1 / 10	133×	7.47e-3	5.69e-2
Androgen biosynthesis CYP17A1	Reactome	1 / 11	121×	8.22e-3	6.07e-2
Insulin processing INS	Reactome	1 / 14	95.3×	1.04e-2	7.05e-2
Hormone signaling INS, VIP	KEGG	2 / 219	12.2×	1.10e-2	7.25e-2
Extracellular matrix organization COL4A5	Reactome	1 / 15	89.0×	1.12e-2	7.34e-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 long-term synaptic potentiation INS, SHANK3	GO:1900273	2 / 24	173×	5.66e-5	1.97e-3 ✓ sig.
cognition INS, SHANK3	GO:0050890	2 / 64	64.9×	4.09e-4	8.35e-3 ✓ sig.
epinephrine secretion VIP	GO:0048242	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
regulation of protein localization INS, VIP	GO:0032880	2 / 89	46.7×	7.90e-4	1.30e-2 ✓ sig.
negative regulation of glycogen catabolic process INS	GO:0045818	1 / 2	1,038×	9.63e-4	1.47e-2 ✓ sig.
guanylate kinase-associated protein clustering SHANK3	GO:0097117	1 / 2	1,038×	9.63e-4	1.47e-2 ✓ sig.
positive regulation of synapse structural plasticity SHANK3	GO:0051835	1 / 3	692×	1.44e-3	1.87e-2 ✓ sig.
positive regulation of nitric-oxide synthase activity INS	GO:0051000	1 / 3	692×	1.44e-3	1.87e-2 ✓ sig.
prolactin secretion VIP	GO:0070459	1 / 3	692×	1.44e-3	1.87e-2 ✓ sig.
olefinic compound metabolic process CYP17A1	GO:0120254	1 / 4	519×	1.93e-3	2.20e-2 ✓ sig.
positive regulation of nitric oxide mediated signal transduction INS	GO:0010750	1 / 4	519×	1.93e-3	2.20e-2 ✓ sig.
striatal medium spiny neuron differentiation SHANK3	GO:0021773	1 / 4	519×	1.93e-3	2.20e-2 ✓ sig.
AMPA glutamate receptor clustering SHANK3	GO:0097113	1 / 5	415×	2.41e-3	2.50e-2 ✓ sig.
NMDA glutamate receptor clustering SHANK3	GO:0097114	1 / 5	415×	2.41e-3	2.50e-2 ✓ sig.
positive regulation of dendritic spine maintenance INS	GO:1902952	1 / 5	415×	2.41e-3	2.50e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
22q13 monosomy syndrome	22q13.3 deletion syndrome	0.400	2	5.06e-8	3.92e-7 ✓ sig.
22q13 monosomy syndrome	Ventricular outflow obstruction	0.333	1	1.30e-4	3.90e-4 ✓ sig.
22q13 monosomy syndrome	phelan-mcdermid syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Hyperkalemia	Ventricular outflow obstruction	0.333	1	1.30e-4	3.90e-4 ✓ sig.
22q13 monosomy syndrome	Hyperkalemia	0.250	1	2.60e-4	6.40e-4 ✓ sig.
22q13.3 deletion syndrome	Ventricular outflow obstruction	0.200	1	2.60e-4	6.40e-4 ✓ sig.
22q13.3 deletion syndrome	phelan-mcdermid syndrome	0.200	1	2.60e-4	6.40e-4 ✓ sig.
sorsby fundus dystrophy	Urinary bladder diseases	0.167	1	3.25e-4	7.58e-4 ✓ sig.
Urinary bladder diseases	Ventricular outflow obstruction	0.167	1	3.25e-4	7.58e-4 ✓ sig.
22q13.3 deletion syndrome	Hyperkalemia	0.167	1	5.19e-4	1.04e-3 ✓ sig.
Hyperkalemia	Urinary bladder diseases	0.143	1	6.49e-4	1.22e-3 ✓ sig.
22q13 monosomy syndrome	Urinary bladder diseases	0.143	1	6.49e-4	1.22e-3 ✓ sig.
22q13.3 deletion syndrome	Urinary bladder diseases	0.111	1	1.30e-3	2.04e-3 ✓ sig.

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