Disease Clusters | GeDiPNet

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Cluster 252

8 diseases · 18 shared-gene connections

8 Diseases

7 Unique genes

0.330 Avg. similarity score

Abnormality of the skin Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Abnormality of the genital system 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.

Abnormality of the genital system Abnormality of the skin Cataract 44, hypotrichosis 14 Cataract-alopecia-sclerodactyly syndrome Alopecia-intellectual disability syndrome Perniola krajewska carnevale syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Abnormality of the skin	6	6	1
Cataract 44, hypotrichosis 14	6	6	1
Cataract-alopecia-sclerodactyly syndrome	6	6	1
Alopecia-intellectual disability syndrome	5	5	2
Perniola krajewska carnevale syndrome	5	5	3
Abnormality of the genital system	3	3	2
Alopecia	3	3	4
Amr syndrome	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
LSS	7 / 8	Abnormality of the genital system, Abnormality of the skin, Alopecia, Alopecia-intellectual disability syndrome and 3 more
AHSG	3 / 8	Alopecia-intellectual disability syndrome, Amr syndrome, Perniola krajewska carnevale 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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
Elastic fibre formation ITGB6	Reactome	1 / 18	95.3×	1.04e-2	5.84e-2
Steroid biosynthesis LSS	KEGG	1 / 20	85.8×	1.16e-2	6.22e-2
Cholesterol biosynthesis LSS	Reactome	1 / 21	81.7×	1.22e-2	6.41e-2
Molecules associated with elastic fibres ITGB6	Reactome	1 / 38	45.2×	2.19e-2	9.03e-2
Activation of gene expression by SREBF (SREBP) LSS	Reactome	1 / 42	40.9×	2.42e-2	9.58e-2
ECM proteoglycans ITGB6	Reactome	1 / 51	33.6×	2.94e-2	1.07e-1
Renin secretion EDNRA	KEGG	1 / 69	24.9×	3.95e-2	1.26e-1
Degradation of the extracellular matrix HTRA1	Reactome	1 / 70	24.5×	4.01e-2	1.28e-1
Integrin cell surface interactions ITGB6	Reactome	1 / 81	21.2×	4.63e-2	1.38e-1
Arrhythmogenic right ventricular cardiomyopathy ITGB6	KEGG	1 / 86	20.0×	4.91e-2	1.43e-1
ECM-receptor interaction ITGB6	KEGG	1 / 89	19.3×	5.07e-2	1.46e-1
Hypertrophic cardiomyopathy ITGB6	KEGG	1 / 99	17.3×	5.63e-2	1.55e-1
Dilated cardiomyopathy ITGB6	KEGG	1 / 105	16.3×	5.96e-2	1.60e-1
Peptide ligand-binding receptors EDNRA	Reactome	1 / 106	16.2×	6.02e-2	1.61e-1
Post-translational protein phosphorylation AHSG	Reactome	1 / 108	15.9×	6.13e-2	1.63e-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 ⇵
triterpenoid biosynthetic process LSS	GO:0016104	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
regulation of protein localization to cell leading edge EDNRA	GO:1905871	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
response to wounding ITGB6, EDNRA	GO:0009611	2 / 81	65.9×	3.84e-4	7.95e-3 ✓ sig.
cellular response to human chorionic gonadotropin stimulus EDNRA	GO:0044751	1 / 2	1,335×	7.49e-4	1.23e-2 ✓ sig.
transforming growth factor beta production ITGB6	GO:0071604	1 / 2	1,335×	7.49e-4	1.23e-2 ✓ sig.
podocyte apoptotic process EDNRA	GO:1903210	1 / 2	1,335×	7.49e-4	1.23e-2 ✓ sig.
cardiac chamber formation EDNRA	GO:0003207	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
semaphorin-plexin signaling pathway involved in axon guidance EDNRA	GO:1902287	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
endothelin receptor signaling pathway involved in heart process EDNRA	GO:0086101	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
pinocytosis AHSG	GO:0006907	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
renal albumin absorption EDNRA	GO:0097018	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
Langerhans cell differentiation ITGB6	GO:0061520	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
atrial cardiac muscle tissue development EDNRA	GO:0003228	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
sympathetic neuron axon guidance EDNRA	GO:0097492	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
neural crest cell fate commitment EDNRA	GO:0014034	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Alopecia-intellectual disability syndrome	Perniola krajewska carnevale syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Cataract 44, hypotrichosis 14	Cataract-alopecia-sclerodactyly syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Abnormality of the skin	Cataract-alopecia-sclerodactyly syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Abnormality of the skin	Cataract 44, hypotrichosis 14	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Abnormality of the genital system	Abnormality of the skin	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Alopecia-intellectual disability syndrome	Cataract 44, hypotrichosis 14	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Alopecia-intellectual disability syndrome	Cataract-alopecia-sclerodactyly syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Alopecia-intellectual disability syndrome	Amr syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormality of the skin	Alopecia-intellectual disability syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormality of the genital system	Cataract 44, hypotrichosis 14	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Abnormality of the genital system	Cataract-alopecia-sclerodactyly syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Amr syndrome	Perniola krajewska carnevale syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cataract-alopecia-sclerodactyly syndrome	Perniola krajewska carnevale syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Abnormality of the skin	Perniola krajewska carnevale syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cataract 44, hypotrichosis 14	Perniola krajewska carnevale syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Alopecia	Cataract 44, hypotrichosis 14	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Abnormality of the skin	Alopecia	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Alopecia	Cataract-alopecia-sclerodactyly syndrome	0.200	1	2.58e-4	5.38e-4 ✓ sig.

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