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 122

10 diseases · 30 shared-gene connections
10 Diseases
18 Unique genes
0.310 Avg. similarity score
Glucose-6-phosphate dehydrogenase deficiency Most-connected disease (9 links)
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Disease Searched: IKBKG-related immunodeficiency with or without ectodermal dysplasia 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 ⇵
Glucose-6-phosphate dehydrogenase deficiency 9 9 5
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema 8 8 2
Autoinflammatory disease, systemic, x-linked 8 8 2
Bloch sulzberger syndrome 7 7 2
G6PD deficiency 6 6 1
anemia, nonspherocytic hemolytic, due to G6PD deficiency 6 6 1
Granulomatous disease 5 5 9
IKBKG-related immunodeficiency with or without ectodermal dysplasia 5 5 1
incontinentia pigmenti 5 5 1
Peritonitis 1 1 7

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

Gene ⇵ Member diseases ⇵ Linked diseases
G6PD 7 / 10 anemia, nonspherocytic hemolytic, due to G6PD deficiency, Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema, Autoinflammatory disease, systemic, x-linked, Bloch sulzberger syndrome and 3 more
IKBKG 6 / 10 Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema, Autoinflammatory disease, systemic, x-linked, Bloch sulzberger syndrome, Glucose-6-phosphate dehydrogenase deficiency and 2 more
IFNG 3 / 10 Glucose-6-phosphate dehydrogenase deficiency, Granulomatous disease, Peritonitis
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 ⇵
Cross-presentation of particulate exogenous antigens (phagosomes)
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 8 417× 2.30e-13 5.04e-11 ✓ sig.
Leishmaniasis
CYBA, CYBB, IFNG, NCF1, NCF2, NCF4, IL10
 KEGG 7 / 78 59.9× 1.11e-11 1.85e-9 ✓ sig.
RHO GTPases Activate NADPH Oxidases
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 24 139× 1.72e-10 2.24e-8 ✓ sig.
Lipid and atherosclerosis
IKBKG, CYBA, CYBB, NCF1, NCF2, NCF4, IL6, GSK3B
 KEGG 8 / 216 24.7× 3.61e-10 4.28e-8 ✓ sig.
ROS and RNS production in phagocytes
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 34 98.1× 1.12e-9 1.17e-7 ✓ sig.
Detoxification of Reactive Oxygen Species
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 34 98.1× 1.12e-9 1.17e-7 ✓ sig.
Prion disease
CYBA, CYBB, NCF1, NCF2, NCF4, IL6, C5, GSK3B
 KEGG 8 / 275 19.4× 2.45e-9 2.36e-7 ✓ sig.
Diabetic cardiomyopathy
G6PD, CYBA, CYBB, NCF1, NCF2, NCF4, GSK3B
 KEGG 7 / 205 22.8× 1.03e-8 8.48e-7 ✓ sig.
VEGFA-VEGFR2 Pathway
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 62 53.8× 2.53e-8 1.87e-6 ✓ sig.
Osteoclast differentiation
IKBKG, CYBA, IFNG, NCF1, NCF2, NCF4
 KEGG 6 / 142 28.2× 4.06e-8 2.85e-6 ✓ sig.
Neutrophil extracellular trap formation
CYBA, CYBB, NCF1, NCF2, NCF4, C5
 KEGG 6 / 192 20.9× 2.44e-7 1.37e-5 ✓ sig.
Leukocyte transendothelial migration
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 116 28.8× 5.97e-7 2.98e-5 ✓ sig.
Fluid shear stress and atherosclerosis
IKBKG, CYBA, IFNG, NCF1, NCF2
 KEGG 5 / 141 23.7× 1.57e-6 6.90e-5 ✓ sig.
Phagosome
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 155 21.5× 2.51e-6 1.03e-4 ✓ sig.
IL-17 signaling pathway
IKBKG, IFNG, IL6, GSK3B
 KEGG 4 / 94 28.4× 9.90e-6 3.22e-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 ⇵
respiratory burst
CYBA, CYBB, NCF1, NCF2, NCF4
 GO:0045730 5 / 15 346× 1.35e-12 5.99e-10 ✓ sig.
superoxide anion generation
CYBA, CYBB, NCF1, NCF2, NCF4
 GO:0042554 5 / 26 200× 2.93e-11 9.75e-9 ✓ sig.
superoxide metabolic process
CYBA, CYBB, NCF1, NCF2
 GO:0006801 4 / 22 189× 4.36e-9 8.14e-7 ✓ sig.
hydrogen peroxide biosynthetic process
CYBA, CYBB, NCF1
 GO:0050665 3 / 11 283× 1.23e-7 1.43e-5 ✓ sig.
innate immune response
IKBKG, CYBA, CYBB, CYBC1, NCF1, NCF2, C5
 GO:0045087 7 / 605 12.0× 8.40e-7 7.18e-5 ✓ sig.
inflammatory response
IKBKG, CYBA, CYBB, NCF1, IL6, C5
 GO:0006954 6 / 467 13.3× 3.39e-6 2.22e-4 ✓ sig.
positive regulation of tumor necrosis factor production
CYBA, CYBB, IFNG, IL6
 GO:0032760 4 / 113 36.7× 3.63e-6 2.34e-4 ✓ sig.
cellular response to L-glutamine
CYBA, CYBB
 GO:1904845 2 / 4 519× 5.25e-6 3.15e-4 ✓ sig.
positive regulation of receptor signaling pathway via JAK-STAT
IL10, IL6, USP1
 GO:0046427 3 / 40 77.9× 7.25e-6 4.08e-4 ✓ sig.
positive regulation of chemokine production
IFNG, IL6, C5
 GO:0032722 3 / 49 63.6× 1.34e-5 6.63e-4 ✓ sig.
response to activity
CYBA, IL10, IL6
 GO:0014823 3 / 52 59.9× 1.61e-5 7.63e-4 ✓ sig.
cell surface receptor signaling pathway via JAK-STAT
IFNG, IL6, USP1
 GO:0007259 3 / 67 46.5× 3.46e-5 1.37e-3 ✓ sig.
positive regulation of endothelial cell proliferation
CYBA, IL10, PPP1R16B
 GO:0001938 3 / 69 45.1× 3.78e-5 1.46e-3 ✓ sig.
response to aldosterone
CYBA, CYBB
 GO:1904044 2 / 10 208× 3.93e-5 1.50e-3 ✓ sig.
positive regulation of MHC class II biosynthetic process
IFNG, IL10
 GO:0045348 2 / 15 138× 9.13e-5 2.83e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema Autoinflammatory disease, systemic, x-linked 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema Bloch sulzberger syndrome 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Autoinflammatory disease, systemic, x-linked Bloch sulzberger syndrome 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema Glucose-6-phosphate dehydrogenase deficiency 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Autoinflammatory disease, systemic, x-linked Glucose-6-phosphate dehydrogenase deficiency 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Bloch sulzberger syndrome Glucose-6-phosphate dehydrogenase deficiency 0.333 2 8.44e-8 5.94e-7 ✓ sig.
Glucose-6-phosphate dehydrogenase deficiency Granulomatous disease 0.154 2 3.03e-6 1.63e-5 ✓ sig.
anemia, nonspherocytic hemolytic, due to G6PD deficiency G6PD deficiency 0.500 1 6.49e-5 2.33e-4 ✓ sig.
IKBKG-related immunodeficiency with or without ectodermal dysplasia incontinentia pigmenti 0.500 1 6.49e-5 2.33e-4 ✓ sig.
anemia, nonspherocytic hemolytic, due to G6PD deficiency Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Bloch sulzberger syndrome incontinentia pigmenti 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Autoinflammatory disease, systemic, x-linked incontinentia pigmenti 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema incontinentia pigmenti 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Bloch sulzberger syndrome IKBKG-related immunodeficiency with or without ectodermal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Autoinflammatory disease, systemic, x-linked IKBKG-related immunodeficiency with or without ectodermal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema IKBKG-related immunodeficiency with or without ectodermal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Bloch sulzberger syndrome G6PD deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Autoinflammatory disease, systemic, x-linked G6PD deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema G6PD deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
anemia, nonspherocytic hemolytic, due to G6PD deficiency Bloch sulzberger syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
anemia, nonspherocytic hemolytic, due to G6PD deficiency Autoinflammatory disease, systemic, x-linked 0.333 1 1.30e-4 3.93e-4 ✓ sig.
G6PD deficiency Glucose-6-phosphate dehydrogenase deficiency 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Glucose-6-phosphate dehydrogenase deficiency IKBKG-related immunodeficiency with or without ectodermal dysplasia 0.167 1 3.25e-4 7.70e-4 ✓ sig.
anemia, nonspherocytic hemolytic, due to G6PD deficiency Glucose-6-phosphate dehydrogenase deficiency 0.167 1 3.25e-4 7.70e-4 ✓ sig.
Glucose-6-phosphate dehydrogenase deficiency incontinentia pigmenti 0.167 1 3.25e-4 7.70e-4 ✓ sig.
G6PD deficiency Granulomatous disease 0.100 1 5.84e-4 1.16e-3 ✓ sig.
anemia, nonspherocytic hemolytic, due to G6PD deficiency Granulomatous disease 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Anhidrotic ectodermal dysplasia with immunodeficiency, osteopetrosis, and lymphedema Granulomatous disease 0.091 1 1.17e-3 1.89e-3 ✓ sig.
Autoinflammatory disease, systemic, x-linked Granulomatous disease 0.091 1 1.17e-3 1.89e-3 ✓ sig.
Glucose-6-phosphate dehydrogenase deficiency Peritonitis 0.083 1 2.27e-3 3.19e-3 ✓ sig.