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Cluster 603

5 diseases · 10 shared-gene connections

5 Diseases

5 Unique genes

0.367 Avg. similarity score

Cholesteatoma 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.

Cholesteatoma Intellectual developmental disorder, autosomal dominant 41 Intellectual disability with autism spectrum disorder Mental retardation, autosomal dominant 41 Pierpont syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Cholesteatoma	4	4	5
Intellectual developmental disorder, autosomal dominant 41	4	4	1
Intellectual disability with autism spectrum disorder	4	4	1
Mental retardation, autosomal dominant 41	4	4	1
Pierpont syndrome	4	4	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
TBL1XR1	5 / 5	Cholesteatoma, Intellectual developmental disorder, autosomal dominant 41, Intellectual disability with autism spectrum disorder, Mental retardation, autosomal dominant 41 and 1 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 ⇵
Coronavirus disease - COVID-19 F13B, IL2	KEGG	2 / 238	20.2×	3.76e-3	2.99e-2 ✓ sig.
RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) IL2	Reactome	1 / 10	240×	4.16e-3	3.21e-2 ✓ sig.
Interleukin-2 signaling IL2	Reactome	1 / 12	200×	4.99e-3	3.64e-2 ✓ sig.
RORA activates gene expression TBL1XR1	Reactome	1 / 18	133×	7.47e-3	4.73e-2 ✓ sig.
Regulation of lipid metabolism by PPARalpha TBL1XR1	Reactome	1 / 20	120×	8.30e-3	5.06e-2
Common Pathway of Fibrin Clot Formation F13B	Reactome	1 / 22	109×	9.13e-3	5.37e-2
Interleukin receptor SHC signaling IL2	Reactome	1 / 27	89.0×	1.12e-2	6.09e-2
Notch-HLH transcription pathway TBL1XR1	Reactome	1 / 28	85.8×	1.16e-2	6.22e-2
Circadian Clock TBL1XR1	Reactome	1 / 28	85.8×	1.16e-2	6.22e-2
NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux TBL1XR1	Reactome	1 / 37	64.9×	1.53e-2	7.35e-2
Allograft rejection IL2	KEGG	1 / 39	61.6×	1.61e-2	7.58e-2
Activation of gene expression by SREBF (SREBP) TBL1XR1	Reactome	1 / 42	57.2×	1.74e-2	7.88e-2
Type I diabetes mellitus IL2	KEGG	1 / 44	54.6×	1.82e-2	8.12e-2
Graft-versus-host disease IL2	KEGG	1 / 45	53.4×	1.86e-2	8.21e-2
Intestinal immune network for IgA production IL2	KEGG	1 / 50	48.0×	2.06e-2	8.75e-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 ⇵
response to tacrolimus IL2	GO:1901327	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
regulation of CD4-positive, alpha-beta T cell proliferation IL2	GO:2000561	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
leukocyte activation involved in immune response IL2	GO:0002366	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
regulation of T cell homeostatic proliferation IL2	GO:0046013	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
positive regulation of plasma cell differentiation IL2	GO:1900100	1 / 4	934×	1.07e-3	1.51e-2 ✓ sig.
positive regulation of tissue remodeling IL2	GO:0034105	1 / 6	623×	1.60e-3	1.88e-2 ✓ sig.
negative regulation of lymphocyte proliferation IL2	GO:0050672	1 / 7	534×	1.87e-3	2.05e-2 ✓ sig.
positive regulation of lymphocyte differentiation IL2	GO:0045621	1 / 8	467×	2.14e-3	2.19e-2 ✓ sig.
regulation of triglyceride metabolic process TBL1XR1	GO:0090207	1 / 8	467×	2.14e-3	2.19e-2 ✓ sig.
blood coagulation, fibrin clot formation F13B	GO:0072378	1 / 9	415×	2.41e-3	2.32e-2 ✓ sig.
negative regulation of T-helper 17 cell differentiation IL2	GO:2000320	1 / 9	415×	2.41e-3	2.32e-2 ✓ sig.
fat pad development TBL1XR1	GO:0060613	1 / 10	374×	2.67e-3	2.46e-2 ✓ sig.
activated T cell proliferation IL2	GO:0050798	1 / 10	374×	2.67e-3	2.46e-2 ✓ sig.
negative regulation of B cell apoptotic process IL2	GO:0002903	1 / 11	340×	2.94e-3	2.58e-2 ✓ sig.
positive regulation of isotype switching to IgG isotypes IL2	GO:0048304	1 / 11	340×	2.94e-3	2.58e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Intellectual developmental disorder, autosomal dominant 41	Pierpont syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual developmental disorder, autosomal dominant 41	Intellectual disability with autism spectrum disorder	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual developmental disorder, autosomal dominant 41	Mental retardation, autosomal dominant 41	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual disability with autism spectrum disorder	Pierpont syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Intellectual disability with autism spectrum disorder	Mental retardation, autosomal dominant 41	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mental retardation, autosomal dominant 41	Pierpont syndrome	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cholesteatoma	Pierpont syndrome	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Cholesteatoma	Intellectual disability with autism spectrum disorder	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Cholesteatoma	Mental retardation, autosomal dominant 41	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Cholesteatoma	Intellectual developmental disorder, autosomal dominant 41	0.167	1	3.23e-4	6.41e-4 ✓ sig.

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