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Cluster 420

5 diseases · 5 shared-gene connections

5 Diseases

3 Unique genes

0.300 Avg. similarity score

Primary bilateral macronodular adrenal hyperplasia Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Macronodular adrenal hyperplasia 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.

Macronodular adrenal hyperplasia Primary bilateral macronodular adrenal hyperplasia Cleft palate psychomotor retardation distinctive facial features palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome Osteoma cutis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Primary bilateral macronodular adrenal hyperplasia	4	4	3
Cleft palate psychomotor retardation distinctive facial features	2	2	1
palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome	2	2	1
Macronodular adrenal hyperplasia	1	1	1
Osteoma cutis	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
KDM1A	3 / 5	Cleft palate psychomotor retardation distinctive facial features, palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome, Primary bilateral macronodular adrenal hyperplasia
ARMC5	2 / 5	Macronodular adrenal hyperplasia, Primary bilateral macronodular adrenal hyperplasia
GNAS	2 / 5	Osteoma cutis, Primary bilateral macronodular adrenal hyperplasia

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 ⇵
Cushing syndrome ARMC5, GNAS	KEGG	2 / 155	51.7×	4.92e-4	8.04e-3 ✓ sig.
Thermogenesis KDM1A, GNAS	KEGG	2 / 234	34.2×	1.12e-3	1.51e-2 ✓ sig.
PKA activation in glucagon signalling GNAS	Reactome	1 / 17	235×	4.24e-3	3.98e-2 ✓ sig.
Prostacyclin signalling through prostacyclin receptor GNAS	Reactome	1 / 19	211×	4.74e-3	4.29e-2 ✓ sig.
Glucagon signaling in metabolic regulation GNAS	Reactome	1 / 26	154×	6.48e-3	5.31e-2
Glucagon-type ligand receptors GNAS	Reactome	1 / 33	121×	8.22e-3	6.20e-2
Glucagon-like Peptide-1 (GLP1) regulates insulin secretion GNAS	Reactome	1 / 36	111×	8.97e-3	6.53e-2
NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux KDM1A	Reactome	1 / 37	108×	9.21e-3	6.66e-2
Vasopressin regulates renal water homeostasis via Aquaporins GNAS	Reactome	1 / 43	93.1×	1.07e-2	7.32e-2
Vasopressin-regulated water reabsorption GNAS	KEGG	1 / 44	91.0×	1.10e-2	7.41e-2
Cocaine addiction GNAS	KEGG	1 / 49	81.7×	1.22e-2	7.92e-2
HDMs demethylate histones KDM1A	Reactome	1 / 50	80.1×	1.24e-2	8.00e-2
Vibrio cholerae infection GNAS	KEGG	1 / 51	78.5×	1.27e-2	8.10e-2
Ovarian steroidogenesis GNAS	KEGG	1 / 52	77.0×	1.29e-2	8.18e-2
Endocrine and other factor-regulated calcium reabsorption GNAS	KEGG	1 / 53	75.5×	1.32e-2	8.29e-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 cold-induced thermogenesis KDM1A, GNAS	GO:0120162	2 / 102	122×	8.82e-5	2.82e-3 ✓ sig.
adrenal cortex development ARMC5	GO:0035801	1 / 1	6,229×	1.61e-4	4.40e-3 ✓ sig.
guanine metabolic process KDM1A	GO:0046098	1 / 2	3,115×	3.21e-4	7.18e-3 ✓ sig.
negative regulation of transcription initiation-coupled chromatin remodeling KDM1A	GO:0160217	1 / 3	2,076×	4.82e-4	9.50e-3 ✓ sig.
adenylate cyclase-activating serotonin receptor signaling pathway GNAS	GO:0007192	1 / 5	1,246×	8.03e-4	1.34e-2 ✓ sig.
hair follicle placode formation GNAS	GO:0060789	1 / 5	1,246×	8.03e-4	1.34e-2 ✓ sig.
response to parathyroid hormone GNAS	GO:0071107	1 / 5	1,246×	8.03e-4	1.34e-2 ✓ sig.
regulation of skeletal muscle contraction GNAS	GO:0014819	1 / 6	1,038×	9.63e-4	1.50e-2 ✓ sig.
response to fungicide KDM1A	GO:0060992	1 / 6	1,038×	9.63e-4	1.50e-2 ✓ sig.
CD4-positive, alpha-beta T cell differentiation ARMC5	GO:0043367	1 / 7	890×	1.12e-3	1.66e-2 ✓ sig.
cellular response to catecholamine stimulus GNAS	GO:0071870	1 / 7	890×	1.12e-3	1.66e-2 ✓ sig.
negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator KDM1A	GO:1902254	1 / 8	779×	1.28e-3	1.79e-2 ✓ sig.
regulation of steroid biosynthetic process ARMC5	GO:0050810	1 / 9	692×	1.44e-3	1.91e-2 ✓ sig.
vascular endothelial cell response to laminar fluid shear stress GNAS	GO:0097700	1 / 9	692×	1.44e-3	1.91e-2 ✓ sig.
cellular response to glucagon stimulus GNAS	GO:0071377	1 / 11	566×	1.76e-3	2.16e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Cleft palate psychomotor retardation distinctive facial features	palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome	0.500	1	6.49e-5	2.32e-4 ✓ sig.
Cleft palate psychomotor retardation distinctive facial features	Primary bilateral macronodular adrenal hyperplasia	0.250	1	1.95e-4	5.32e-4 ✓ sig.
Macronodular adrenal hyperplasia	Primary bilateral macronodular adrenal hyperplasia	0.250	1	1.95e-4	5.32e-4 ✓ sig.
Osteoma cutis	Primary bilateral macronodular adrenal hyperplasia	0.250	1	1.95e-4	5.32e-4 ✓ sig.
palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome	Primary bilateral macronodular adrenal hyperplasia	0.250	1	1.95e-4	5.32e-4 ✓ sig.

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