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Cluster 338

6 diseases · 8 shared-gene connections

6 Diseases

22 Unique genes

0.223 Avg. similarity score

Brown tendon sheath syndrome Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Parathyroid 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.

Parathyroid disease Brown tendon sheath syndrome Osteolysis, hereditary, of carpal bones with or without nephropathy Hyperparathyroidism TUBB4A-related neurologic disorder Whispering dysphonia

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Brown tendon sheath syndrome	4	4	3
Osteolysis, hereditary, of carpal bones with or without nephropathy	3	3	1
Parathyroid disease	3	3	4
Hyperparathyroidism	2	2	19
TUBB4A-related neurologic disorder	2	2	1
Whispering dysphonia	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MAFB	4 / 6	Brown tendon sheath syndrome, Hyperparathyroidism, Osteolysis, hereditary, of carpal bones with or without nephropathy, Parathyroid disease
TUBB4A	3 / 6	Brown tendon sheath syndrome, TUBB4A-related neurologic disorder, Whispering dysphonia
C1ORF185	2 / 6	Hyperparathyroidism, Parathyroid disease
TMEM14B	2 / 6	Hyperparathyroidism, Parathyroid disease

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 ⇵
Parathyroid hormone synthesis, secretion and action MAFB, VDR, GCM2, CASR, PTH1R, PTH	KEGG	6 / 115	28.5×	4.45e-8	3.10e-6 ✓ sig.
PTK6 Regulates Cell Cycle CCND1, CDKN1B	Reactome	2 / 6	182×	4.78e-5	1.20e-3 ✓ sig.
Endocrine and other factor-regulated calcium reabsorption VDR, PTH1R, PTH	KEGG	3 / 53	30.9×	1.18e-4	2.49e-3 ✓ sig.
Class B/2 (Secretin family receptors) PTH1R, PTH	Reactome	2 / 18	60.7×	4.81e-4	7.65e-3 ✓ sig.
Rheumatoid arthritis PTH, ACP5, IL6	KEGG	3 / 95	17.2×	6.62e-4	9.80e-3 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications CCND1, CDKN1B, IL6	KEGG	3 / 101	16.2×	7.91e-4	1.12e-2 ✓ sig.
Estrogen-dependent nuclear events downstream of ESR-membrane signaling CCND1, CDKN1B	Reactome	2 / 23	47.5×	7.92e-4	1.12e-2 ✓ sig.
Post-translational protein phosphorylation MEN1, APOL1, IL6	Reactome	3 / 108	15.2×	9.62e-4	1.30e-2 ✓ sig.
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) MEN1, APOL1, IL6	Reactome	3 / 125	13.1×	1.47e-3	1.81e-2 ✓ sig.
RHO GTPases activate IQGAPs TUBB4A, MEN1	Reactome	2 / 32	34.1×	1.54e-3	1.87e-2 ✓ sig.
ADORA2B mediated anti-inflammatory cytokines production PTH1R, PTH, IL6	Reactome	3 / 128	12.8×	1.57e-3	1.90e-2 ✓ sig.
FoxO signaling pathway CCND1, CDKN1B, IL6	KEGG	3 / 133	12.3×	1.75e-3	2.07e-2 ✓ sig.
Measles CCND1, CDKN1B, IL6	KEGG	3 / 139	11.8×	1.99e-3	2.27e-2 ✓ sig.
African trypanosomiasis APOL1, IL6	KEGG	2 / 37	29.5×	2.05e-3	2.32e-2 ✓ sig.
Transcriptional Regulation by VENTX CCND1, IL6	Reactome	2 / 38	28.7×	2.16e-3	2.41e-2 ✓ sig.

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

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
intracellular calcium ion homeostasis VDR, GCM2, CASR, PTH1R, PTH	GO:0006874	5 / 113	37.6×	1.79e-7	1.97e-5 ✓ sig.
bone resorption PTH1R, PTH, ACP5	GO:0045453	3 / 26	98.0×	3.62e-6	2.33e-4 ✓ sig.
negative regulation of cell population proliferation VDR, CDC73, MEN1, PTH1R, CDKN1B, IL6	GO:0008285	6 / 444	11.5×	9.39e-6	5.02e-4 ✓ sig.
adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway CASR, PTH	GO:0140582	2 / 5	340×	1.32e-5	6.53e-4 ✓ sig.
calcium ion homeostasis TRPV6, PTH, ALPL	GO:0055074	3 / 42	60.7×	1.58e-5	7.50e-4 ✓ sig.
skeletal system development VDR, PTH1R, PTH, ALPL	GO:0001501	4 / 151	22.5×	2.68e-5	1.13e-3 ✓ sig.
positive regulation of inositol phosphate biosynthetic process PTH1R, PTH	GO:0060732	2 / 7	243×	2.77e-5	1.16e-3 ✓ sig.
response to glucocorticoid CCND1, ALPL, IL6	GO:0051384	3 / 53	48.1×	3.19e-5	1.29e-3 ✓ sig.
response to calcium ion CASR, CCND1, TRPV6	GO:0051592	3 / 55	46.3×	3.57e-5	1.40e-3 ✓ sig.
bone mineralization PTH1R, PTH, ALPL	GO:0030282	3 / 56	45.5×	3.77e-5	1.46e-3 ✓ sig.
regulation of G1/S transition of mitotic cell cycle CCND1, TMEM14B, CDKN1B	GO:2000045	3 / 57	44.7×	3.98e-5	1.52e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II MAFB, VDR, CDC73, GCM2, MEN1, PTH, IL6, EBF2	GO:0045944	8 / 1,208	5.6×	4.21e-5	1.59e-3 ✓ sig.
negative regulation of cyclin-dependent protein serine/threonine kinase activity MEN1, CDKN1B	GO:0045736	2 / 9	189×	4.74e-5	1.74e-3 ✓ sig.
response to fibroblast growth factor CASR, PTH	GO:0071774	2 / 11	154×	7.23e-5	2.38e-3 ✓ sig.
negative regulation of lipid storage CRP, IL6	GO:0010888	2 / 12	142×	8.67e-5	2.72e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Hyperparathyroidism	Parathyroid disease	0.143	3	6.37e-9	5.32e-8 ✓ sig.
TUBB4A-related neurologic disorder	Whispering dysphonia	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Brown tendon sheath syndrome	Whispering dysphonia	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Brown tendon sheath syndrome	TUBB4A-related neurologic disorder	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Brown tendon sheath syndrome	Osteolysis, hereditary, of carpal bones with or without nephropathy	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Osteolysis, hereditary, of carpal bones with or without nephropathy	Parathyroid disease	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Brown tendon sheath syndrome	Parathyroid disease	0.143	1	7.79e-4	1.40e-3 ✓ sig.
Hyperparathyroidism	Osteolysis, hereditary, of carpal bones with or without nephropathy	0.050	1	1.23e-3	1.98e-3 ✓ sig.

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