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Cluster 242

8 diseases · 14 shared-gene connections

8 Diseases

25 Unique genes

0.207 Avg. similarity score

16q24.3 microdeletion syndrome Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Prieto 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.

Prieto syndrome 16q24.3 microdeletion syndrome Kbg syndrome Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome Astigmatism Congenital retrognathism

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
16q24.3 microdeletion syndrome	5	5	1
Kbg syndrome	5	5	1
Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome	5	5	1
Astigmatism	4	4	7
Congenital retrognathism	4	4	6
Metabolic bone disorder	3	3	14
Dyschromatopsia	1	1	2
Prieto syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
ANKRD11	6 / 8	16q24.3 microdeletion syndrome, Astigmatism, Congenital retrognathism, Kbg syndrome and 2 more
EYS	2 / 8	Astigmatism, Dyschromatopsia
PHF3	2 / 8	Astigmatism, Dyschromatopsia
WNK3	2 / 8	Congenital retrognathism, Prieto syndrome

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 ⇵
Vitamin D (calciferol) metabolism CYP2R1, GC, LRP2	Reactome	3 / 11	131×	1.30e-6	5.24e-5 ✓ sig.
Steroid biosynthesis LBR, CYP2R1, DHCR7	KEGG	3 / 20	72.1×	8.87e-6	2.64e-4 ✓ sig.
Endocrine resistance ESR1, IGF1, MMP2	KEGG	3 / 99	14.6×	1.10e-3	1.21e-2 ✓ sig.
Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) SLC9A6	Reactome	1 / 1	480×	2.08e-3	1.96e-2 ✓ sig.
Defective CYP2R1 causes Rickets vitamin D-dependent 1B (VDDR1B) CYP2R1	Reactome	1 / 1	480×	2.08e-3	1.96e-2 ✓ sig.
Defective CYP27A1 causes Cerebrotendinous xanthomatosis (CTX) CYP27A1	Reactome	1 / 1	480×	2.08e-3	1.96e-2 ✓ sig.
Defective ABCC8 can cause hypoglycemias and hyperglycemias ABCC8	Reactome	1 / 2	240×	4.16e-3	3.21e-2 ✓ sig.
Sodium-coupled phosphate cotransporters SLC20A1	Reactome	1 / 2	240×	4.16e-3	3.21e-2 ✓ sig.
Cholesterol metabolism CYP27A1, LRP2	KEGG	2 / 51	18.8×	4.98e-3	3.64e-2 ✓ sig.
Extra-nuclear estrogen signaling ESR1, MMP2	Reactome	2 / 58	16.6×	6.40e-3	4.29e-2 ✓ sig.
ATP sensitive Potassium channels ABCC8	Reactome	1 / 4	120×	8.30e-3	5.06e-2
Cholesterol biosynthesis via desmosterol DHCR7	Reactome	1 / 4	120×	8.30e-3	5.06e-2
Cholesterol biosynthesis via lathosterol DHCR7	Reactome	1 / 4	120×	8.30e-3	5.06e-2
Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) IGF1	Reactome	1 / 4	120×	8.30e-3	5.06e-2
Proteoglycans in cancer ESR1, IGF1, MMP2	KEGG	3 / 204	7.1×	8.43e-3	5.12e-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 ⇵
vitamin D metabolic process CYP27A1, CYP2R1, GC, LRP2	GO:0042359	4 / 12	249×	1.22e-9	2.77e-7 ✓ sig.
face morphogenesis ANKRD11, ARID5B, MMP2	GO:0060325	3 / 33	68.0×	1.12e-5	5.96e-4 ✓ sig.
calcitriol biosynthetic process from calciol CYP27A1, CYP2R1	GO:0036378	2 / 5	299×	1.71e-5	8.22e-4 ✓ sig.
bone mineralization involved in bone maturation IGF1, PHOSPHO1	GO:0035630	2 / 6	249×	2.57e-5	1.11e-3 ✓ sig.
skeletal system morphogenesis ANKRD11, ARID5B, MMP2	GO:0048705	3 / 45	49.8×	2.89e-5	1.22e-3 ✓ sig.
prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ESR1, IGF1	GO:0060527	2 / 7	214×	3.59e-5	1.44e-3 ✓ sig.
positive regulation of fibroblast proliferation CTC1, ESR1, IGF1	GO:0048146	3 / 55	40.8×	5.30e-5	1.93e-3 ✓ sig.
vitamin transport GC, LRP2	GO:0051180	2 / 10	149×	7.68e-5	2.54e-3 ✓ sig.
regulation of monoatomic cation transmembrane transport GRIN2B, WNK3	GO:1904062	2 / 10	149×	7.68e-5	2.54e-3 ✓ sig.
vagina development ESR1, LRP2	GO:0060068	2 / 10	149×	7.68e-5	2.54e-3 ✓ sig.
prostate gland epithelium morphogenesis IGF1, MMP2	GO:0060740	2 / 10	149×	7.68e-5	2.54e-3 ✓ sig.
steroid biosynthetic process LBR, CYP27A1, DHCR7	GO:0006694	3 / 65	34.5×	8.75e-5	2.80e-3 ✓ sig.
negative regulation of smooth muscle cell apoptotic process ESR1, IGF1	GO:0034392	2 / 14	107×	1.55e-4	4.24e-3 ✓ sig.
cholesterol metabolic process LBR, CYP27A1, DHCR7	GO:0008203	3 / 107	21.0×	3.83e-4	7.94e-3 ✓ sig.
cell population proliferation MCM7, IGF1, LRP2, SLC20A1	GO:0008283	4 / 263	11.4×	3.84e-4	7.95e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Astigmatism	Dyschromatopsia	0.250	2	1.75e-7	1.18e-6 ✓ sig.
16q24.3 microdeletion syndrome	Kbg syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
16q24.3 microdeletion syndrome	Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Kbg syndrome	Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
16q24.3 microdeletion syndrome	Congenital retrognathism	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Congenital retrognathism	Kbg syndrome	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Congenital retrognathism	Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome	0.143	1	3.87e-4	7.33e-4 ✓ sig.
Congenital retrognathism	Prieto syndrome	0.143	1	3.87e-4	7.33e-4 ✓ sig.
16q24.3 microdeletion syndrome	Astigmatism	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Astigmatism	Kbg syndrome	0.125	1	4.52e-4	8.26e-4 ✓ sig.
Astigmatism	Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome	0.125	1	4.52e-4	8.26e-4 ✓ sig.
16q24.3 microdeletion syndrome	Metabolic bone disorder	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Kbg syndrome	Metabolic bone disorder	0.067	1	9.04e-4	1.41e-3 ✓ sig.
Metabolic bone disorder	Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome	0.067	1	9.04e-4	1.41e-3 ✓ sig.

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