Disease Clusters | GeDiPNet

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Cluster 475

6 diseases · 14 shared-gene connections

6 Diseases

7 Unique genes

0.333 Avg. similarity score

Dc type 4 and 5 Most-connected disease (5 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.

Dc type 4 and 5 Dyskeratosis congenita, autosomal dominant 4 Dyskeratosis congenita, autosomal recessive 5 Dyskeratosiscongenita, autosomal dominant 4 Telomere syndrome X-linked dyskeratosis congenita

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Dc type 4 and 5	5	5	1
Dyskeratosis congenita, autosomal dominant 4	5	5	1
Dyskeratosis congenita, autosomal recessive 5	5	5	1
Dyskeratosiscongenita, autosomal dominant 4	5	5	1
Telomere syndrome	4	4	5
X-linked dyskeratosis congenita	4	4	3

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

Gene ⇵	Member diseases ⇵	Linked diseases
RTEL1	6 / 6	Dc type 4 and 5, Dyskeratosis congenita, autosomal dominant 4, Dyskeratosis congenita, autosomal recessive 5, Dyskeratosiscongenita, autosomal dominant 4 and 2 more

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 Extension By Telomerase RTEL1, TERT, WRAP53, DKC1	Reactome	4 / 16	429×	7.33e-11	8.96e-9 ✓ sig.
Telomere C-strand synthesis initiation POLA2	Reactome	1 / 7	245×	4.07e-3	3.17e-2 ✓ sig.
DNA replication initiation POLA2	Reactome	1 / 8	214×	4.65e-3	3.48e-2 ✓ sig.
Processive synthesis on the lagging strand POLA2	Reactome	1 / 10	172×	5.82e-3	4.03e-2 ✓ sig.
Inhibition of replication initiation of damaged DNA by RB1/E2F1 POLA2	Reactome	1 / 10	172×	5.82e-3	4.03e-2 ✓ sig.
rRNA modification in the nucleus and cytosol DKC1	Reactome	1 / 12	143×	6.97e-3	4.53e-2 ✓ sig.
Polymerase switching POLA2	Reactome	1 / 14	123×	8.13e-3	5.01e-2
Removal of the Flap Intermediate POLA2	Reactome	1 / 14	123×	8.13e-3	5.01e-2
KSRP (KHSRP) binds and destabilizes mRNA PARN	Reactome	1 / 15	114×	8.71e-3	5.22e-2
Polymerase switching on the C-strand of the telomere POLA2	Reactome	1 / 17	101×	9.87e-3	5.65e-2
ATF4 activates genes in response to endoplasmic reticulum stress PARN	Reactome	1 / 18	95.3×	1.04e-2	5.84e-2
Deadenylation of mRNA PARN	Reactome	1 / 24	71.5×	1.39e-2	6.94e-2
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) RTEL1	Reactome	1 / 26	66.0×	1.51e-2	7.27e-2
Cargo concentration in the ER CD59	Reactome	1 / 33	52.0×	1.91e-2	8.33e-2
Activation of the pre-replicative complex POLA2	Reactome	1 / 33	52.0×	1.91e-2	8.33e-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 ⇵
positive regulation of telomere maintenance via telomerase PARN, WRAP53, DKC1	GO:0032212	3 / 23	348×	5.68e-8	7.89e-6 ✓ sig.
telomere maintenance via telomerase TERT, WRAP53, DKC1	GO:0007004	3 / 24	334×	6.49e-8	8.84e-6 ✓ sig.
box H/ACA sno(s)RNA 3'-end processing PARN, DKC1	GO:0000495	2 / 2	2,670×	1.20e-7	1.48e-5 ✓ sig.
protein localization to Cajal body WRAP53, DKC1	GO:1904867	2 / 2	2,670×	1.20e-7	1.48e-5 ✓ sig.
telomerase RNA stabilization PARN, DKC1	GO:0090669	2 / 4	1,335×	7.21e-7	6.58e-5 ✓ sig.
regulation of telomerase RNA localization to Cajal body PARN, DKC1	GO:1904872	2 / 4	1,335×	7.21e-7	6.58e-5 ✓ sig.
scaRNA localization to Cajal body WRAP53, DKC1	GO:0090666	2 / 5	1,068×	1.20e-6	9.99e-5 ✓ sig.
RNA modification PARN, DKC1	GO:0009451	2 / 17	314×	1.63e-5	7.92e-4 ✓ sig.
telomere maintenance RTEL1, TERT	GO:0000723	2 / 66	80.9×	2.55e-4	6.04e-3 ✓ sig.
regulation of RNA stability PARN	GO:0043487	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
DNA strand displacement RTEL1	GO:0000732	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
negative regulation of telomere maintenance in response to DNA damage RTEL1	GO:1904506	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
positive regulation of telomeric loop disassembly RTEL1	GO:1904535	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
DNA strand elongation TERT	GO:0022616	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
siRNA transcription TERT	GO:0140745	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Dc type 4 and 5	Dyskeratosiscongenita, autosomal dominant 4	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dc type 4 and 5	Dyskeratosis congenita, autosomal recessive 5	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dc type 4 and 5	Dyskeratosis congenita, autosomal dominant 4	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dyskeratosis congenita, autosomal dominant 4	Dyskeratosiscongenita, autosomal dominant 4	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dyskeratosis congenita, autosomal dominant 4	Dyskeratosis congenita, autosomal recessive 5	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dyskeratosis congenita, autosomal recessive 5	Dyskeratosiscongenita, autosomal dominant 4	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Dc type 4 and 5	X-linked dyskeratosis congenita	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Dyskeratosis congenita, autosomal dominant 4	X-linked dyskeratosis congenita	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Dyskeratosis congenita, autosomal recessive 5	X-linked dyskeratosis congenita	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Dyskeratosiscongenita, autosomal dominant 4	X-linked dyskeratosis congenita	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Dc type 4 and 5	Telomere syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Dyskeratosis congenita, autosomal dominant 4	Telomere syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Dyskeratosis congenita, autosomal recessive 5	Telomere syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Dyskeratosiscongenita, autosomal dominant 4	Telomere syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.

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