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Cluster 381

5 diseases · 5 shared-gene connections

5 Diseases

9 Unique genes

0.197 Avg. similarity score

Cerebroretinal microangiopathy with calcifications and cysts Most-connected disease (3 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: spermatogenic failure 18 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.

spermatogenic failure 18 Cerebroretinal microangiopathy with calcifications and cysts Tumor predisposition syndrome Congenital chromosomal disease Coats plus syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cerebroretinal microangiopathy with calcifications and cysts	3	3	4
Tumor predisposition syndrome	3	3	6
Congenital chromosomal disease	2	2	1
Coats plus syndrome	1	1	2
spermatogenic failure 18	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
POT1	3 / 5	Cerebroretinal microangiopathy with calcifications and cysts, Congenital chromosomal disease, Tumor predisposition syndrome
CTC1	2 / 5	Cerebroretinal microangiopathy with calcifications and cysts, Coats plus syndrome
DNAH1	2 / 5	spermatogenic failure 18, Tumor predisposition syndrome
STN1	2 / 5	Cerebroretinal microangiopathy with calcifications and cysts, Coats plus 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 ⇵
Telomere C-strand synthesis initiation CTC1, STN1	Reactome	2 / 7	381×	1.05e-5	3.55e-4 ✓ sig.
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks BAP1, CHEK2	Reactome	2 / 76	35.1×	1.38e-3	1.78e-2 ✓ sig.
Recognition and association of DNA glycosylase with site containing an affected pyrimidine MBD4	Reactome	1 / 8	167×	5.98e-3	5.03e-2
Cleavage of the damaged pyrimidine MBD4	Reactome	1 / 8	167×	5.98e-3	5.03e-2
Displacement of DNA glycosylase by APEX1 MBD4	Reactome	1 / 9	148×	6.73e-3	5.44e-2
Stabilization of p53 CHEK2	Reactome	1 / 11	121×	8.22e-3	6.20e-2
Purine ribonucleoside monophosphate biosynthesis PFAS	Reactome	1 / 12	111×	8.96e-3	6.53e-2
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex CHEK2	Reactome	1 / 12	111×	8.96e-3	6.53e-2
Telomere Extension By Telomerase POT1	Reactome	1 / 16	83.4×	1.19e-2	7.79e-2
Regulation of TP53 Activity through Methylation CHEK2	Reactome	1 / 19	70.2×	1.42e-2	8.63e-2
Homologous DNA Pairing and Strand Exchange BRCA2	Reactome	1 / 25	53.4×	1.86e-2	1.02e-1
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) BRCA2	Reactome	1 / 26	51.3×	1.93e-2	1.04e-1
Resolution of D-loop Structures through Holliday Junction Intermediates BRCA2	Reactome	1 / 33	40.4×	2.45e-2	1.19e-1
Regulation of TP53 Degradation CHEK2	Reactome	1 / 36	37.1×	2.67e-2	1.25e-1
Presynaptic phase of homologous DNA pairing and strand exchange BRCA2	Reactome	1 / 39	34.2×	2.89e-2	1.30e-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 ⇵
telomere capping CTC1, STN1, POT1	GO:0016233	3 / 12	519×	1.70e-8	2.67e-6 ✓ sig.
negative regulation of telomere maintenance via telomerase CTC1, STN1, POT1	GO:0032211	3 / 22	283×	1.18e-7	1.41e-5 ✓ sig.
telomere maintenance CTC1, STN1, POT1	GO:0000723	3 / 66	94.4×	3.48e-6	2.29e-4 ✓ sig.
establishment of protein localization to telomere POT1, BRCA2	GO:0070200	2 / 7	593×	4.32e-6	2.73e-4 ✓ sig.
telomere maintenance via telomere lengthening CTC1, STN1	GO:0010833	2 / 9	461×	7.41e-6	4.20e-4 ✓ sig.
replicative senescence CTC1, CHEK2	GO:0090399	2 / 16	260×	2.47e-5	1.07e-3 ✓ sig.
hematopoietic stem cell proliferation CTC1, BRCA2	GO:0071425	2 / 25	166×	6.15e-5	2.14e-3 ✓ sig.
response to gamma radiation BRCA2, CHEK2	GO:0010332	2 / 27	154×	7.19e-5	2.42e-3 ✓ sig.
positive regulation of DNA replication CTC1, STN1	GO:0045740	2 / 29	143×	8.32e-5	2.70e-3 ✓ sig.
DNA damage response CTC1, BRCA2, MBD4, CHEK2	GO:0006974	4 / 577	14.4×	1.00e-4	3.10e-3 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator BRCA2, CHEK2	GO:0042771	2 / 33	126×	1.08e-4	3.27e-3 ✓ sig.
DNA damage response, signal transduction by p53 class mediator BRCA2, CHEK2	GO:0030330	2 / 48	86.5×	2.30e-4	5.67e-3 ✓ sig.
chromosome organization CTC1, BRCA2	GO:0051276	2 / 51	81.4×	2.60e-4	6.18e-3 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage BRCA2, CHEK2	GO:0008630	2 / 54	76.9×	2.91e-4	6.70e-3 ✓ sig.
positive regulation of DNA strand elongation POT1	GO:0060383	1 / 1	2,076×	4.82e-4	9.50e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Cerebroretinal microangiopathy with calcifications and cysts	Coats plus syndrome	0.400	2	5.06e-8	3.72e-7 ✓ sig.
Cerebroretinal microangiopathy with calcifications and cysts	Congenital chromosomal disease	0.200	1	2.60e-4	6.48e-4 ✓ sig.
Congenital chromosomal disease	Tumor predisposition syndrome	0.143	1	3.90e-4	8.64e-4 ✓ sig.
spermatogenic failure 18	Tumor predisposition syndrome	0.143	1	3.90e-4	8.64e-4 ✓ sig.
Cerebroretinal microangiopathy with calcifications and cysts	Tumor predisposition syndrome	0.100	1	1.56e-3	2.37e-3 ✓ sig.

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