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Cluster 324

6 diseases · 6 shared-gene connections

6 Diseases

24 Unique genes

0.119 Avg. similarity score

Osteolysis Most-connected disease (3 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Camptodactyly-arthropathy-coxa vara-pericarditis syndrome 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.

Camptodactyly-arthropathy-coxa vara-pericarditis syndrome Osteolysis Bone resorption Contracture Hyaline fibromatosis autosomal recessive osteopetrosis 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Osteolysis	3	3	7
Bone resorption	2	2	10
Contracture	2	2	10
Hyaline fibromatosis	2	2	1
autosomal recessive osteopetrosis 2	2	2	1
Camptodactyly-arthropathy-coxa vara-pericarditis syndrome	1	1	2

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

Gene ⇵	Member diseases ⇵	Linked diseases
ANTXR2	3 / 6	Contracture, Hyaline fibromatosis, Osteolysis
TNFSF11	3 / 6	autosomal recessive osteopetrosis 2, Bone resorption, Osteolysis
PRG4	2 / 6	Camptodactyly-arthropathy-coxa vara-pericarditis syndrome, Contracture
PTHLH	2 / 6	Bone resorption, Osteolysis
TNFRSF11B	2 / 6	Bone resorption, Osteolysis

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 ⇵
Rheumatoid arthritis CXCL2, PTH, TNFSF11, TNF	KEGG	4 / 95	21.1×	3.46e-5	9.18e-4 ✓ sig.
Cytokine-cytokine receptor interaction BMP7, CXCL2, TNFRSF11B, TNFSF11, TNF	KEGG	5 / 298	8.4×	2.62e-4	4.72e-3 ✓ sig.
Human papillomavirus infection COL2A1, WNT7B, IBSP, SPP1, TNF	KEGG	5 / 333	7.5×	4.38e-4	7.10e-3 ✓ sig.
Integrin cell surface interactions COL2A1, IBSP, SPP1	Reactome	3 / 81	18.5×	5.40e-4	8.35e-3 ✓ sig.
Class B/2 (Secretin family receptors) PTH, PTHLH	Reactome	2 / 18	55.6×	5.74e-4	8.77e-3 ✓ sig.
ECM-receptor interaction COL2A1, IBSP, SPP1	KEGG	3 / 89	16.9×	7.11e-4	1.04e-2 ✓ sig.
Endogenous sterols AHR, CYP19A1	Reactome	2 / 25	40.0×	1.12e-3	1.46e-2 ✓ sig.
NF-kappa B signaling pathway CXCL2, TNFSF11, TNF	KEGG	3 / 105	14.3×	1.15e-3	1.50e-2 ✓ sig.
Parathyroid hormone synthesis, secretion and action PTH, PTHLH, TNFSF11	KEGG	3 / 115	13.1×	1.49e-3	1.83e-2 ✓ sig.
TNFs bind their physiological receptors TNFRSF11B, TNFSF11	Reactome	2 / 29	34.5×	1.50e-3	1.84e-2 ✓ sig.
Signaling by PDGF COL2A1, SPP1	Reactome	2 / 33	30.3×	1.95e-3	2.23e-2 ✓ sig.
Defective CYP19A1 causes Aromatase excess syndrome (AEXS) CYP19A1	Reactome	1 / 1	500×	2.00e-3	2.28e-2 ✓ sig.
Osteoclast differentiation TNFRSF11B, TNFSF11, TNF	KEGG	3 / 142	10.6×	2.73e-3	2.87e-2 ✓ sig.
Interleukin-10 signaling CXCL2, TNF	Reactome	2 / 47	21.3×	3.92e-3	3.70e-2 ✓ sig.
Legionellosis CXCL2, TNF	KEGG	2 / 56	17.9×	5.52e-3	4.67e-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 ⇵
ossification BMP7, COL2A1, TNFSF11, IBSP, SPP1	GO:0001503	5 / 110	35.4×	2.51e-7	2.62e-5 ✓ sig.
skeletal system development BMP7, COL2A1, PTH, PTHLH, TNFRSF11B	GO:0001501	5 / 151	25.8×	1.21e-6	9.70e-5 ✓ sig.
positive regulation of estradiol secretion CYP19A1, SPP1	GO:2000866	2 / 2	779×	1.58e-6	1.21e-4 ✓ sig.
response to vitamin D BMP7, PTH, SPP1	GO:0033280	3 / 21	111×	2.44e-6	1.70e-4 ✓ sig.
response to macrophage colony-stimulating factor SPP1, TNF	GO:0036005	2 / 4	389×	9.47e-6	5.05e-4 ✓ sig.
cAMP metabolic process PTH, PTHLH	GO:0046058	2 / 4	389×	9.47e-6	5.05e-4 ✓ sig.
androgen catabolic process CYP19A1, SPP1	GO:0006710	2 / 5	311×	1.58e-5	7.50e-4 ✓ sig.
adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway PTH, PTHLH	GO:0140582	2 / 5	311×	1.58e-5	7.50e-4 ✓ sig.
extracellular matrix organization TNFRSF11B, ADAMTSL2, IBSP, TNF	GO:0030198	4 / 145	21.5×	3.27e-5	1.31e-3 ✓ sig.
chorio-allantoic fusion BMP7, WNT7B	GO:0060710	2 / 7	222×	3.31e-5	1.32e-3 ✓ sig.
bone mineralization PTH, PTHLH, IBSP	GO:0030282	3 / 56	41.7×	4.93e-5	1.79e-3 ✓ sig.
cellular response to molecule of bacterial origin AHR, TNF	GO:0071219	2 / 9	173×	5.66e-5	1.98e-3 ✓ sig.
embryonic skeletal joint morphogenesis BMP7, COL2A1	GO:0060272	2 / 11	142×	8.63e-5	2.72e-3 ✓ sig.
system development COL2A1, EPHB1, WNT7B	GO:0048731	3 / 74	31.6×	1.14e-4	3.34e-3 ✓ sig.
positive regulation of heterotypic cell-cell adhesion BMP7, TNF	GO:0034116	2 / 13	120×	1.22e-4	3.52e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Bone resorption	Osteolysis	0.200	3	6.89e-9	5.75e-8 ✓ sig.
autosomal recessive osteopetrosis 2	Osteolysis	0.125	1	4.55e-4	9.72e-4 ✓ sig.
Hyaline fibromatosis	Osteolysis	0.125	1	4.55e-4	9.72e-4 ✓ sig.
autosomal recessive osteopetrosis 2	Bone resorption	0.091	1	6.49e-4	1.24e-3 ✓ sig.
Contracture	Hyaline fibromatosis	0.091	1	6.49e-4	1.24e-3 ✓ sig.
Camptodactyly-arthropathy-coxa vara-pericarditis syndrome	Contracture	0.083	1	1.30e-3	2.06e-3 ✓ sig.

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