Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 163

10 diseases · 23 shared-gene connections
10 Diseases
20 Unique genes
0.261 Avg. similarity score
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Most-connected disease (7 links)
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Disease Searched: Immunodeficiency 123 with hpv-related verrucosis 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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency 7 7 1
Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation 7 7 1
Lymphadenopathy 7 7 1
Haploinsufficiency 5 5 2
Mycosis fungoides 5 5 3
Anti-glomerular basement membrane disease 4 4 4
Enteropathy 4 4 3
Autoimmune hemolytic anemia 3 3 5
Berylliosis 2 2 10
Immunodeficiency 123 with hpv-related verrucosis 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CTLA4 8 / 10 Anti-glomerular basement membrane disease, Autoimmune hemolytic anemia, Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency, Enteropathy and 4 more
CD28 3 / 10 Berylliosis, Immunodeficiency 123 with hpv-related verrucosis, Mycosis fungoides
HLA-DPB1 2 / 10 Anti-glomerular basement membrane disease, Berylliosis
HLA-DRB1 2 / 10 Anti-glomerular basement membrane disease, Berylliosis
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 ⇵
Rheumatoid arthritis
CTLA4, HLA-DPB1, HLA-DRB1, CD28, IL6, TGFB1, TNF
 KEGG 7 / 95 44.2× 1.10e-10 1.21e-8 ✓ sig.
Graft-versus-host disease
HLA-DPB1, HLA-DRB1, CD28, IL6, TNF
 KEGG 5 / 45 66.7× 8.73e-9 6.25e-7 ✓ sig.
Intestinal immune network for IgA production
HLA-DPB1, HLA-DRB1, CD28, IL6, TGFB1
 KEGG 5 / 50 60.1× 1.51e-8 1.02e-6 ✓ sig.
Inflammatory bowel disease
HLA-DPB1, HLA-DRB1, IL6, TGFB1, TNF
 KEGG 5 / 66 45.5× 6.25e-8 3.54e-6 ✓ sig.
Leishmaniasis
FCGR3A, HLA-DPB1, HLA-DRB1, TGFB1, TNF
 KEGG 5 / 78 38.5× 1.46e-7 7.43e-6 ✓ sig.
Tuberculosis
FCGR3A, HLA-DPB1, HLA-DRB1, IL6, TGFB1, TNF
 KEGG 6 / 181 19.9× 3.51e-7 1.58e-5 ✓ sig.
Allograft rejection
HLA-DPB1, HLA-DRB1, CD28, TNF
 KEGG 4 / 39 61.6× 4.43e-7 1.94e-5 ✓ sig.
Hematopoietic cell lineage
HLA-DPB1, HLA-DRB1, IL2RA, IL6, TNF
 KEGG 5 / 100 30.0× 5.08e-7 2.18e-5 ✓ sig.
Type I diabetes mellitus
HLA-DPB1, HLA-DRB1, CD28, TNF
 KEGG 4 / 44 54.6× 7.27e-7 2.96e-5 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
SOCS1, IL6, TGFB1, TNF, TNFRSF1B
 Reactome 5 / 108 27.8× 7.46e-7 3.03e-5 ✓ sig.
Th17 cell differentiation
HLA-DPB1, HLA-DRB1, IL2RA, IL6, TGFB1
 KEGG 5 / 109 27.5× 7.81e-7 3.15e-5 ✓ sig.
Toxoplasmosis
HLA-DPB1, HLA-DRB1, SOCS1, TGFB1, TNF
 KEGG 5 / 112 26.8× 8.94e-7 3.55e-5 ✓ sig.
Human T-cell leukemia virus 1 infection
HLA-DPB1, HLA-DRB1, IL2RA, IL6, TGFB1, TNF
 KEGG 6 / 224 16.1× 1.23e-6 4.65e-5 ✓ sig.
Autoimmune thyroid disease
CTLA4, HLA-DPB1, HLA-DRB1, CD28
 KEGG 4 / 54 44.5× 1.68e-6 6.07e-5 ✓ sig.
Systemic lupus erythematosus
FCGR3A, HLA-DPB1, HLA-DRB1, CD28, TNF
 KEGG 5 / 140 21.4× 2.70e-6 9.09e-5 ✓ 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
CTLA4, FCGR3A, HLA-DPB1, HLA-DRB1, TLR8, CD28, IL2RA, IL6, TNF
 GO:0006955 9 / 543 15.5× 1.75e-9 3.78e-7 ✓ sig.
positive regulation of T cell proliferation
HLA-DPB1, BTNL2, CD28, IL2RA, IL6
 GO:0042102 5 / 67 69.7× 7.57e-9 1.39e-6 ✓ sig.
T cell receptor signaling pathway
CTLA4, HLA-DPB1, HLA-DRB1, BTNL2, CD28
 GO:0050852 5 / 121 38.6× 1.50e-7 1.76e-5 ✓ sig.
negative regulation of T cell proliferation
CTLA4, HLA-DRB1, IL2RA, TGFB1
 GO:0042130 4 / 51 73.3× 2.31e-7 2.52e-5 ✓ sig.
humoral immune response
HLA-DRB1, CD28, IL6, TNF
 GO:0006959 4 / 58 64.4× 3.90e-7 3.90e-5 ✓ sig.
regulation of T cell proliferation
CTLA4, CD28, TNFRSF1B
 GO:0042129 3 / 17 165× 7.06e-7 6.38e-5 ✓ sig.
mononuclear cell proliferation
ACE, TGFB1
 GO:0032943 2 / 3 623× 3.26e-6 2.20e-4 ✓ sig.
liver regeneration
IL6, TGFB1, TNF
 GO:0097421 3 / 29 96.7× 3.76e-6 2.46e-4 ✓ sig.
positive regulation of interleukin-6 production
TLR8, IL6, TGFB1, TNF
 GO:0032755 4 / 103 36.3× 3.94e-6 2.55e-4 ✓ sig.
regulatory T cell differentiation
CD28, TGFB1
 GO:0045066 2 / 4 467× 6.52e-6 3.81e-4 ✓ sig.
positive regulation of mononuclear cell migration
TGFB1, TNF
 GO:0071677 2 / 4 467× 6.52e-6 3.81e-4 ✓ sig.
inflammatory response
TLR8, IL2RA, IL6, TGFB1, TNF, TNFRSF1B
 GO:0006954 6 / 467 12.0× 6.79e-6 3.93e-4 ✓ sig.
positive regulation of T cell activation
HLA-DPB1, HLA-DRB1, CD28
 GO:0050870 3 / 45 62.3× 1.45e-5 7.06e-4 ✓ sig.
vascular endothelial growth factor production
IL6, TNF
 GO:0010573 2 / 6 311× 1.63e-5 7.72e-4 ✓ sig.
response to activity
GCLM, IL6, TNF
 GO:0014823 3 / 52 53.9× 2.24e-5 9.84e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Anti-glomerular basement membrane disease Berylliosis 0.154 2 2.25e-6 1.31e-5 ✓ sig.
Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation Lymphadenopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Lymphadenopathy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Haploinsufficiency Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Haploinsufficiency Lymphadenopathy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Haploinsufficiency 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lymphadenopathy Mycosis fungoides 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Immunodeficiency 123 with hpv-related verrucosis Mycosis fungoides 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation Mycosis fungoides 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Enteropathy Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Enteropathy Lymphadenopathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Enteropathy 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency Mycosis fungoides 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Anti-glomerular basement membrane disease Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Anti-glomerular basement membrane disease Lymphadenopathy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Anti-glomerular basement membrane disease Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Autoimmune hemolytic anemia Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Autoimmune hemolytic anemia Lymphadenopathy 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Autoimmune hemolytic anemia Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Haploinsufficiency Mycosis fungoides 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Enteropathy Haploinsufficiency 0.200 1 3.87e-4 7.33e-4 ✓ sig.
Berylliosis Immunodeficiency 123 with hpv-related verrucosis 0.091 1 6.46e-4 1.09e-3 ✓ sig.