Disease Clusters | GeDiPNet

Cluster 309

7 diseases · 16 shared-gene connections

7 Diseases

2 Unique genes

0.437 Avg. similarity score

Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Short stature, palatal anomalies, congenital heart disease, and skeletal malformations 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.

Short stature, palatal anomalies, congenital heart disease, and skeletal malformations Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 20p12.3 microdeletion syndrome Hfe hemochromatosis, modifier of Right ventricle hypoplasia Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	6	6	2
20p12.3 microdeletion syndrome	5	5	1
Hfe hemochromatosis, modifier of	5	5	1
Right ventricle hypoplasia	5	5	1
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1	5	5	1
Short stature, palatal anomalies, congenital heart disease, and skeletal malformations	5	5	1
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
BMP2	6 / 7	20p12.3 microdeletion syndrome, Hfe hemochromatosis, modifier of, Right ventricle hypoplasia, Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies and 2 more
SCUBE3	2 / 7	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies, Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2

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 ⇵
Transcriptional regulation by RUNX2 BMP2	Reactome	1 / 12	500×	2.00e-3	1.90e-2 ✓ sig.
Signaling by BMP BMP2	Reactome	1 / 28	214×	4.66e-3	3.48e-2 ✓ sig.
Molecules associated with elastic fibres BMP2	Reactome	1 / 38	158×	6.32e-3	4.25e-2 ✓ sig.
Basal cell carcinoma BMP2	KEGG	1 / 63	95.3×	1.05e-2	5.84e-2
Degradation of the extracellular matrix SCUBE3	Reactome	1 / 70	85.8×	1.16e-2	6.22e-2
TGF-beta signaling pathway BMP2	KEGG	1 / 108	55.6×	1.79e-2	8.04e-2
Hippo signaling pathway BMP2	KEGG	1 / 157	38.2×	2.60e-2	9.97e-2
Cytokine-cytokine receptor interaction BMP2	KEGG	1 / 298	20.2×	4.90e-2	1.43e-1
Pathways in cancer BMP2	KEGG	1 / 533	11.3×	8.68e-2	1.99e-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 ⇵
positive regulation of osteoblast differentiation BMP2, SCUBE3	GO:0045669	2 / 78	240×	1.72e-5	8.24e-4 ✓ sig.
negative regulation of calcium-independent cell-cell adhesion BMP2	GO:0051042	1 / 1	9,344×	1.07e-4	3.25e-3 ✓ sig.
endodermal-mesodermal cell signaling BMP2	GO:0003133	1 / 2	4,672×	2.14e-4	5.31e-3 ✓ sig.
cardiac atrium formation BMP2	GO:0003210	1 / 2	4,672×	2.14e-4	5.31e-3 ✓ sig.
cardiocyte differentiation BMP2	GO:0035051	1 / 2	4,672×	2.14e-4	5.31e-3 ✓ sig.
mesenchymal cell proliferation involved in ureteric bud development BMP2	GO:0072138	1 / 2	4,672×	2.14e-4	5.31e-3 ✓ sig.
regulation of cardiac muscle cell differentiation BMP2	GO:2000725	1 / 2	4,672×	2.14e-4	5.31e-3 ✓ sig.
positive regulation of extracellular matrix constituent secretion BMP2	GO:0003331	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
positive regulation of phosphatase activity BMP2	GO:0010922	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
embryonic heart tube anterior/posterior pattern specification BMP2	GO:0035054	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
corticotropin hormone secreting cell differentiation BMP2	GO:0060128	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
positive regulation of bone mineralization involved in bone maturation BMP2	GO:1900159	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
negative regulation of aldosterone biosynthetic process BMP2	GO:0032348	1 / 4	2,336×	4.28e-4	8.53e-3 ✓ sig.
cardiac jelly development BMP2	GO:1905072	1 / 4	2,336×	4.28e-4	8.53e-3 ✓ sig.
atrioventricular canal morphogenesis BMP2	GO:1905222	1 / 4	2,336×	4.28e-4	8.53e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
20p12.3 microdeletion syndrome	Right ventricle hypoplasia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
20p12.3 microdeletion syndrome	Short stature, palatal anomalies, congenital heart disease, and skeletal malformations	0.500	1	6.46e-5	1.98e-4 ✓ sig.
20p12.3 microdeletion syndrome	Hfe hemochromatosis, modifier of	0.500	1	6.46e-5	1.98e-4 ✓ sig.
20p12.3 microdeletion syndrome	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Hfe hemochromatosis, modifier of	Right ventricle hypoplasia	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Hfe hemochromatosis, modifier of	Short stature, palatal anomalies, congenital heart disease, and skeletal malformations	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Hfe hemochromatosis, modifier of	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Right ventricle hypoplasia	Short stature, palatal anomalies, congenital heart disease, and skeletal malformations	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Right ventricle hypoplasia	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1	Short stature, palatal anomalies, congenital heart disease, and skeletal malformations	0.500	1	6.46e-5	1.98e-4 ✓ sig.
20p12.3 microdeletion syndrome	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Hfe hemochromatosis, modifier of	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Right ventricle hypoplasia	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	Short stature, palatal anomalies, congenital heart disease, and skeletal malformations	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2	0.333	1	1.29e-4	3.27e-4 ✓ sig.

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