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 133

10 diseases · 18 shared-gene connections
10 Diseases
27 Unique genes
0.182 Avg. similarity score
Hyper-igm immunodeficiency syndrome Most-connected disease (7 links)
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Disease Searched: immunodeficiency, common variable, 2 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 ⇵
Hyper-igm immunodeficiency syndrome 7 7 7
Hyper-immunoglobulin m syndrome 6 6 4
Blast crisis 5 5 2
Hodgkin disease 4 4 17
Hyper-immunoglobulin syndrome 4 4 2
X-linked hyper-igm syndrome 3 3 1
Bloom syndrome 2 2 2
Chromosome 22q11.2 microdeletion syndrome 2 2 3
Myelogenous leukemia 2 2 3
immunodeficiency, common variable, 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AICDA 4 / 10 Blast crisis, Hyper-igm immunodeficiency syndrome, Hyper-immunoglobulin m syndrome, Hyper-immunoglobulin syndrome
CD40 4 / 10 Hodgkin disease, Hyper-igm immunodeficiency syndrome, Hyper-immunoglobulin m syndrome, Hyper-immunoglobulin syndrome
CD40LG 4 / 10 Hodgkin disease, Hyper-igm immunodeficiency syndrome, Hyper-immunoglobulin m syndrome, X-linked hyper-igm syndrome
BCR 3 / 10 Blast crisis, Chromosome 22q11.2 microdeletion syndrome, Myelogenous leukemia
UNG 3 / 10 Bloom syndrome, Hyper-igm immunodeficiency syndrome, Hyper-immunoglobulin m syndrome
MAPK1 2 / 10 Chromosome 22q11.2 microdeletion syndrome, Hodgkin disease
TNFRSF13B 2 / 10 Hyper-igm immunodeficiency syndrome, immunodeficiency, common variable, 2
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 ⇵
Primary immunodeficiency
AICDA, UNG, CD40, CD40LG, TNFRSF13B, IKBKG
 KEGG 6 / 38 70.2× 1.87e-10 2.40e-8 ✓ sig.
Chronic myeloid leukemia
BCR, ABL1, CRKL, MAPK1, NFKBIA, IKBKG
 KEGG 6 / 77 34.7× 1.52e-8 1.22e-6 ✓ sig.
NF-kappa B signaling pathway
CD40, CD40LG, CFLAR, ICAM1, NFKBIA, IKBKG
 KEGG 6 / 105 25.4× 9.86e-8 6.46e-6 ✓ sig.
Lipid and atherosclerosis
MAPK1, CD40, CD40LG, ICAM1, IFNA2, NFKBIA, IKBKG
 KEGG 7 / 216 14.4× 3.61e-7 2.01e-5 ✓ sig.
Cytokine-cytokine receptor interaction
CD40, CD40LG, CSF3, IFNA2, TNFRSF8, TNFSF8, TNFRSF13B
 KEGG 7 / 298 10.4× 3.13e-6 1.31e-4 ✓ sig.
Toll-like receptor signaling pathway
MAPK1, CD40, IFNA2, NFKBIA, IKBKG
 KEGG 5 / 109 20.4× 3.87e-6 1.57e-4 ✓ sig.
Intestinal immune network for IgA production
AICDA, CD40, CD40LG, TNFRSF13B
 KEGG 4 / 50 35.6× 4.35e-6 1.72e-4 ✓ sig.
Malaria
CD40, CD40LG, CSF3, ICAM1
 KEGG 4 / 50 35.6× 4.35e-6 1.72e-4 ✓ sig.
Toxoplasmosis
MAPK1, CD40, CD40LG, NFKBIA, IKBKG
 KEGG 5 / 112 19.9× 4.42e-6 1.75e-4 ✓ sig.
TNF signaling pathway
MAPK1, CFLAR, ICAM1, NFKBIA, IKBKG
 KEGG 5 / 119 18.7× 5.95e-6 2.23e-4 ✓ sig.
Pathways in cancer
BCR, ABL1, CRKL, MAPK1, GSTP1, IFNA2, NFKBIA, IKBKG
 KEGG 8 / 533 6.7× 1.50e-5 4.78e-4 ✓ sig.
Viral myocarditis
ABL1, CD40, CD40LG, ICAM1
 KEGG 4 / 70 25.4× 1.68e-5 5.25e-4 ✓ sig.
Hepatitis C
MAPK1, CFLAR, IFNA2, NFKBIA, IKBKG
 KEGG 5 / 159 14.0× 2.44e-5 7.19e-4 ✓ sig.
TNFs bind their physiological receptors
TNFRSF8, TNFSF8, TNFRSF13B
 Reactome 3 / 29 46.0× 3.56e-5 9.79e-4 ✓ sig.
Influenza A
MAPK1, ICAM1, IFNA2, NFKBIA, IKBKG
 KEGG 5 / 173 12.9× 3.65e-5 9.98e-4 ✓ 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 ⇵
cellular response to lipopolysaccharide
AICDA, BCR, ABL1, CD40, CSF3, GSTP1
 GO:0071222 6 / 187 22.2× 2.30e-7 2.48e-5 ✓ sig.
T cell receptor signaling pathway
ABL1, CRKL, MAPK1, GATA3, IKBKG
 GO:0050852 5 / 121 28.6× 7.54e-7 6.66e-5 ✓ sig.
thymus development
ABL1, CRKL, MAPK1, GATA3
 GO:0048538 4 / 50 55.4× 7.60e-7 6.70e-5 ✓ sig.
positive regulation of canonical NF-kappaB signal transduction
ABL1, CD40, CD40LG, CFLAR, REL, IKBKG
 GO:0043123 6 / 232 17.9× 8.17e-7 7.10e-5 ✓ sig.
canonical NF-kappaB signal transduction
ABL1, NFKBIA, REL, IKBKG
 GO:0007249 4 / 62 44.7× 1.82e-6 1.36e-4 ✓ sig.
isotype switching
AICDA, UNG, CD40LG
 GO:0045190 3 / 19 109× 2.57e-6 1.79e-4 ✓ sig.
inflammatory response
CD40, CD40LG, GATA3, IFNA2, NFKBIA, REL, IKBKG
 GO:0006954 7 / 467 10.4× 3.35e-6 2.23e-4 ✓ sig.
positive regulation of endothelial cell apoptotic process
CD40, CD40LG, PTPN1
 GO:2000353 3 / 29 71.6× 9.59e-6 5.14e-4 ✓ sig.
positive regulation of extracellular matrix organization
ABL1, CFLAR
 GO:1903055 2 / 4 346× 1.20e-5 6.11e-4 ✓ sig.
immune effector process
ABL1, ICAM1
 GO:0002252 2 / 4 346× 1.20e-5 6.11e-4 ✓ sig.
response to exogenous dsRNA
MAPK1, IFNA2, NFKBIA
 GO:0043330 3 / 34 61.1× 1.56e-5 7.51e-4 ✓ sig.
cellular response to tumor necrosis factor
MAPK1, CD40, GATA3, NFKBIA
 GO:0071356 4 / 107 25.9× 1.61e-5 7.69e-4 ✓ sig.
response to ethanol
CSF3, GATA3, GSTP1, G6PD
 GO:0045471 4 / 110 25.2× 1.80e-5 8.37e-4 ✓ sig.
vascular endothelial cell response to oscillatory fluid shear stress
ABL1, PTPN1
 GO:0097706 2 / 5 277× 2.01e-5 9.14e-4 ✓ sig.
B cell proliferation
ABL1, CD40, CD40LG
 GO:0042100 3 / 38 54.6× 2.19e-5 9.78e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyper-igm immunodeficiency syndrome Hyper-immunoglobulin m syndrome 0.500 4 1.49e-14 2.07e-13 ✓ sig.
Hyper-immunoglobulin m syndrome Hyper-immunoglobulin syndrome 0.400 2 5.06e-8 3.72e-7 ✓ sig.
Hyper-igm immunodeficiency syndrome Hyper-immunoglobulin syndrome 0.250 2 1.77e-7 1.19e-6 ✓ sig.
Hodgkin disease Hyper-immunoglobulin m syndrome 0.100 2 6.87e-6 3.50e-5 ✓ sig.
Hodgkin disease Hyper-igm immunodeficiency syndrome 0.087 2 2.40e-5 1.13e-4 ✓ sig.
Blast crisis Hyper-immunoglobulin syndrome 0.250 1 2.60e-4 6.48e-4 ✓ sig.
Hyper-immunoglobulin m syndrome X-linked hyper-igm syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Blast crisis Myelogenous leukemia 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Blast crisis Chromosome 22q11.2 microdeletion syndrome 0.200 1 3.90e-4 8.64e-4 ✓ sig.
Hyper-igm immunodeficiency syndrome immunodeficiency, common variable, 2 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Hyper-igm immunodeficiency syndrome X-linked hyper-igm syndrome 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Bloom syndrome Hyper-immunoglobulin m syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Blast crisis Hyper-immunoglobulin m syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Chromosome 22q11.2 microdeletion syndrome Myelogenous leukemia 0.167 1 5.84e-4 1.15e-3 ✓ sig.
Bloom syndrome Hyper-igm immunodeficiency syndrome 0.111 1 9.09e-4 1.57e-3 ✓ sig.
Blast crisis Hyper-igm immunodeficiency syndrome 0.111 1 9.09e-4 1.57e-3 ✓ sig.
Hodgkin disease X-linked hyper-igm syndrome 0.056 1 1.10e-3 1.82e-3 ✓ sig.
Hodgkin disease Hyper-immunoglobulin syndrome 0.053 1 2.21e-3 3.11e-3 ✓ sig.