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Cluster 612

5 diseases · 7 shared-gene connections

5 Diseases

2 Unique genes

0.405 Avg. similarity score

Xfe progeroid syndrome Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Xfe progeroid syndrome Facial dysmorphism, immunodeficiency, livedo, and short stature Fils syndrome Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency Xeroderma pigmentosum group F

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Xfe progeroid syndrome	4	4	2
Facial dysmorphism, immunodeficiency, livedo, and short stature	3	3	1
Fils syndrome	3	3	1
Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency	3	3	1
Xeroderma pigmentosum group F	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
POLE	4 / 5	Facial dysmorphism, immunodeficiency, livedo, and short stature, Fils syndrome, Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency, Xfe progeroid syndrome
ERCC4	2 / 5	Xeroderma pigmentosum group F, Xfe progeroid 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 ⇵
Dual Incision in GG-NER ERCC4, POLE	Reactome	2 / 41	293×	1.14e-5	3.24e-4 ✓ sig.
Nucleotide excision repair ERCC4, POLE	KEGG	2 / 63	191×	2.71e-5	6.69e-4 ✓ sig.
Dual incision in TC-NER ERCC4, POLE	Reactome	2 / 66	182×	2.97e-5	7.19e-4 ✓ sig.
DNA replication initiation POLE	Reactome	1 / 8	751×	1.33e-3	1.41e-2 ✓ sig.
PCNA-Dependent Long Patch Base Excision Repair POLE	Reactome	1 / 21	286×	3.49e-3	2.83e-2 ✓ sig.
Gap-filling DNA repair synthesis and ligation in GG-NER POLE	Reactome	1 / 25	240×	4.16e-3	3.21e-2 ✓ sig.
Recognition of DNA damage by PCNA-containing replication complex POLE	Reactome	1 / 30	200×	4.99e-3	3.64e-2 ✓ sig.
Termination of translesion DNA synthesis POLE	Reactome	1 / 32	188×	5.32e-3	3.80e-2 ✓ sig.
Activation of the pre-replicative complex POLE	Reactome	1 / 33	182×	5.49e-3	3.87e-2 ✓ sig.
DNA replication POLE	KEGG	1 / 36	167×	5.99e-3	4.10e-2 ✓ sig.
HDR through Single Strand Annealing (SSA) ERCC4	Reactome	1 / 37	162×	6.15e-3	4.18e-2 ✓ sig.
Fanconi Anemia Pathway ERCC4	Reactome	1 / 40	150×	6.65e-3	4.39e-2 ✓ sig.
Formation of Incision Complex in GG-NER ERCC4	Reactome	1 / 43	140×	7.15e-3	4.61e-2 ✓ sig.
Base excision repair POLE	KEGG	1 / 44	136×	7.31e-3	4.67e-2 ✓ sig.
HDR through Homologous Recombination (HRR) POLE	Reactome	1 / 48	125×	7.98e-3	4.94e-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 ⇵
nucleotide-excision repair involved in interstrand cross-link repair ERCC4	GO:1901255	1 / 2	4,672×	2.14e-4	5.31e-3 ✓ sig.
telomeric DNA-containing double minutes formation ERCC4	GO:0061819	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
negative regulation of protection from non-homologous end joining at telomere ERCC4	GO:1905765	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
DNA replication proofreading POLE	GO:0045004	1 / 3	3,115×	3.21e-4	7.04e-3 ✓ sig.
leading strand elongation POLE	GO:0006272	1 / 4	2,336×	4.28e-4	8.53e-3 ✓ sig.
DNA repair ERCC4, POLE	GO:0006281	2 / 420	44.5×	5.04e-4	9.55e-3 ✓ sig.
negative regulation of telomere maintenance ERCC4	GO:0032205	1 / 5	1,869×	5.35e-4	9.88e-3 ✓ sig.
nucleotide-excision repair, DNA gap filling POLE	GO:0006297	1 / 6	1,557×	6.42e-4	1.11e-2 ✓ sig.
DNA damage response ERCC4, POLE	GO:0006974	2 / 577	32.4×	9.52e-4	1.42e-2 ✓ sig.
negative regulation of telomere maintenance via telomere lengthening ERCC4	GO:1904357	1 / 11	849×	1.18e-3	1.59e-2 ✓ sig.
UV protection ERCC4	GO:0009650	1 / 12	779×	1.28e-3	1.67e-2 ✓ sig.
base-excision repair, gap-filling POLE	GO:0006287	1 / 14	667×	1.50e-3	1.82e-2 ✓ sig.
resolution of meiotic recombination intermediates ERCC4	GO:0000712	1 / 17	550×	1.82e-3	2.02e-2 ✓ sig.
DNA synthesis involved in DNA repair POLE	GO:0000731	1 / 23	406×	2.46e-3	2.36e-2 ✓ sig.
DNA biosynthetic process POLE	GO:0071897	1 / 32	292×	3.42e-3	2.78e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Facial dysmorphism, immunodeficiency, livedo, and short stature	Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Facial dysmorphism, immunodeficiency, livedo, and short stature	Fils syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Fils syndrome	Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Facial dysmorphism, immunodeficiency, livedo, and short stature	Xfe progeroid syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Fils syndrome	Xfe progeroid syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, genital anomalies, and immunodeficiency	Xfe progeroid syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Xeroderma pigmentosum group F	Xfe progeroid syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.

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