Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 405

5 diseases · 6 shared-gene connections

5 Diseases

14 Unique genes

0.167 Avg. similarity score

Lymphoproliferative 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.

Lymphoproliferative syndrome X-linked lymphoproliferative syndrome X-linked lymphoproliferative disease due to SH2D1A deficiency X-linked lymphoproliferative disease due to XIAP deficiency severe combined immunodeficiency due to CD70 deficiency

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Lymphoproliferative syndrome	4	4	14
X-linked lymphoproliferative syndrome	3	3	2
X-linked lymphoproliferative disease due to SH2D1A deficiency	2	2	1
X-linked lymphoproliferative disease due to XIAP deficiency	2	2	1
severe combined immunodeficiency due to CD70 deficiency	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SH2D1A	3 / 5	Lymphoproliferative syndrome, X-linked lymphoproliferative disease due to SH2D1A deficiency, X-linked lymphoproliferative syndrome
XIAP	3 / 5	Lymphoproliferative syndrome, X-linked lymphoproliferative disease due to XIAP deficiency, X-linked lymphoproliferative syndrome
CD70	2 / 5	Lymphoproliferative syndrome, severe combined immunodeficiency due to CD70 deficiency

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 ⇵
Cytokine-cytokine receptor interaction CCL22, IFNG, IL17A, CD70, FAS, CD27	KEGG	6 / 298	17.3×	5.64e-7	2.98e-5 ✓ sig.
Graft-versus-host disease IFNG, FAS, KIR3DS1	KEGG	3 / 45	57.2×	1.74e-5	5.33e-4 ✓ sig.
Necroptosis IFNG, XIAP, FAS, STAT3	KEGG	4 / 159	21.6×	2.67e-5	7.55e-4 ✓ sig.
Inflammatory bowel disease IFNG, IL17A, STAT3	KEGG	3 / 66	39.0×	5.53e-5	1.39e-3 ✓ sig.
Antigen processing and presentation IFNG, KIR3DS1, TAP2	KEGG	3 / 81	31.8×	1.02e-4	2.29e-3 ✓ sig.
RIPK1-mediated regulated necrosis XIAP, FAS	Reactome	2 / 16	107×	1.50e-4	3.11e-3 ✓ sig.
Interleukin-4 and Interleukin-13 signaling CCL22, IL17A, STAT3	Reactome	3 / 108	23.8×	2.40e-4	4.50e-3 ✓ sig.
Th17 cell differentiation IFNG, IL17A, STAT3	KEGG	3 / 109	23.6×	2.46e-4	4.59e-3 ✓ sig.
Toxoplasmosis IFNG, XIAP, STAT3	KEGG	3 / 112	23.0×	2.67e-4	4.90e-3 ✓ sig.
Natural killer cell mediated cytotoxicity IFNG, SH2D1A, FAS	KEGG	3 / 133	19.4×	4.42e-4	7.24e-3 ✓ sig.
TNFs bind their physiological receptors CD70, CD27	Reactome	2 / 29	59.2×	5.03e-4	8.00e-3 ✓ sig.
Hepatitis C IFNG, FAS, STAT3	KEGG	3 / 159	16.2×	7.45e-4	1.09e-2 ✓ sig.
African trypanosomiasis IFNG, FAS	KEGG	2 / 37	46.4×	8.21e-4	1.17e-2 ✓ sig.
Allograft rejection IFNG, FAS	KEGG	2 / 39	44.0×	9.12e-4	1.27e-2 ✓ sig.
Herpes simplex virus 1 infection IFNG, FAS, TAP2	KEGG	3 / 182	14.1×	1.10e-3	1.46e-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 ⇵
immune response CCL22, IFNG, IL17A, CD70, FAS, KIR3DS1, STAT3	GO:0006955	7 / 543	17.2×	4.84e-8	6.61e-6 ✓ sig.
extrinsic apoptotic signaling pathway IFNG, CD70, FAS, CD27	GO:0097191	4 / 57	93.7×	7.61e-8	9.56e-6 ✓ sig.
adaptive immune memory response involving T cells and B cells CD70, CD27	GO:0090717	2 / 3	890×	1.56e-6	1.18e-4 ✓ sig.
CD27 signaling pathway CD70, CD27	GO:0160162	2 / 5	534×	5.21e-6	3.10e-4 ✓ sig.
positive regulation of phagocytosis IFNG, SLC11A1, STAT3	GO:0050766	3 / 58	69.0×	1.01e-5	5.25e-4 ✓ sig.
positive regulation of interleukin-23 production IFNG, IL17A	GO:0032747	2 / 7	381×	1.09e-5	5.58e-4 ✓ sig.
positive regulation of interleukin-1 beta production IFNG, IL17A, STAT3	GO:0032731	3 / 66	60.7×	1.49e-5	7.14e-4 ✓ sig.
T cell activation ITK, CD70, CD27	GO:0042110	3 / 76	52.7×	2.28e-5	9.93e-4 ✓ sig.
negative regulation of inflammatory response to wounding IL17A, STAT3	GO:0106015	2 / 10	267×	2.34e-5	1.01e-3 ✓ sig.
adaptive immune response IFNG, IL17A, SH2D1A, ITK, TAP2	GO:0002250	5 / 507	13.2×	2.36e-5	1.02e-3 ✓ sig.
positive regulation of cytokine production IFNG, ITK, SLC11A1	GO:0001819	3 / 81	49.4×	2.76e-5	1.15e-3 ✓ sig.
interleukin-2-mediated signaling pathway IFNG, STAT3	GO:0038110	2 / 12	222×	3.43e-5	1.35e-3 ✓ sig.
positive regulation of interleukin-6 production IFNG, IL17A, STAT3	GO:0032755	3 / 103	38.9×	5.66e-5	1.97e-3 ✓ sig.
positive regulation of tumor necrosis factor production IFNG, IL17A, STAT3	GO:0032760	3 / 113	35.4×	7.47e-5	2.44e-3 ✓ sig.
apoptotic process IFNG, IL17A, XIAP, FAS, CD27	GO:0006915	5 / 747	8.9×	1.49e-4	4.08e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Lymphoproliferative syndrome	X-linked lymphoproliferative syndrome	0.133	2	7.68e-7	4.83e-6 ✓ sig.
X-linked lymphoproliferative disease due to SH2D1A deficiency	X-linked lymphoproliferative syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
X-linked lymphoproliferative disease due to XIAP deficiency	X-linked lymphoproliferative syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Lymphoproliferative syndrome	severe combined immunodeficiency due to CD70 deficiency	0.067	1	9.09e-4	1.56e-3 ✓ sig.
Lymphoproliferative syndrome	X-linked lymphoproliferative disease due to SH2D1A deficiency	0.067	1	9.09e-4	1.56e-3 ✓ sig.
Lymphoproliferative syndrome	X-linked lymphoproliferative disease due to XIAP deficiency	0.067	1	9.09e-4	1.56e-3 ✓ sig.

Disease Clusters?