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 217

9 diseases · 17 shared-gene connections
9 Diseases
9 Unique genes
0.335 Avg. similarity score
Granulomatous disease Most-connected disease (7 links)
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Disease Searched: Granulomatous disease, chronic, autosomal recessive, 5 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 ⇵
Granulomatous disease 7 7 9
Anemia, nonspherocytic hemolytic 5 5 1
G6PD deficiency 5 5 1
Hemolytic anemia, g6pd deficient (favism) 5 5 1
Infections 5 5 1
Anemia, congenital, non-spherocytic hemolytic, 1 4 4 1
Chronic granulomatous disease, x-linked 1 1 1
Granulomatous disease, chronic, autosomal recessive, 5 1 1 1
Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type iii 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
G6PD 6 / 9 Anemia, congenital, non-spherocytic hemolytic, 1, Anemia, nonspherocytic hemolytic, G6PD deficiency, Granulomatous disease and 2 more
CYBB 2 / 9 Chronic granulomatous disease, x-linked, Granulomatous disease
CYBC1 2 / 9 Granulomatous disease, Granulomatous disease, chronic, autosomal recessive, 5
NCF4 2 / 9 Granulomatous disease, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type iii
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 / 8 834× 3.39e-15 8.62e-13 ✓ sig.
RHO GTPases Activate NADPH Oxidases
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 24 278× 2.56e-12 3.75e-10 ✓ sig.
Leishmaniasis
CYBA, CYBB, IFNG, NCF1, NCF2, NCF4
 KEGG 6 / 78 103× 5.10e-12 7.00e-10 ✓ sig.
ROS and RNS production in phagocytes
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 34 196× 1.67e-11 2.06e-9 ✓ sig.
Detoxification of Reactive Oxygen Species
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 34 196× 1.67e-11 2.06e-9 ✓ sig.
VEGFA-VEGFR2 Pathway
CYBA, CYBB, NCF1, NCF2, NCF4
 Reactome 5 / 62 108× 3.86e-10 3.48e-8 ✓ sig.
Diabetic cardiomyopathy
CYBA, CYBB, G6PD, NCF1, NCF2, NCF4
 KEGG 6 / 205 39.1× 1.85e-9 1.43e-7 ✓ sig.
Leukocyte transendothelial migration
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 116 57.5× 9.42e-9 6.22e-7 ✓ sig.
Osteoclast differentiation
CYBA, IFNG, NCF1, NCF2, NCF4
 KEGG 5 / 142 47.0× 2.61e-8 1.52e-6 ✓ sig.
Phagocytosis
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 155 43.0× 4.06e-8 2.24e-6 ✓ sig.
Neutrophil extracellular trap formation
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 192 34.8× 1.19e-7 5.79e-6 ✓ sig.
Lipid and atherosclerosis
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 216 30.9× 2.14e-7 9.64e-6 ✓ sig.
Prion disease
CYBA, CYBB, NCF1, NCF2, NCF4
 KEGG 5 / 275 24.3× 7.10e-7 2.75e-5 ✓ sig.
Fluid shear stress and atherosclerosis
CYBA, IFNG, NCF1, NCF2
 KEGG 4 / 141 37.9× 2.19e-6 7.27e-5 ✓ sig.
Chemical carcinogenesis - reactive oxygen species
CYBA, NCF1, NCF2
 KEGG 3 / 227 17.6× 5.15e-4 6.32e-3 ✓ 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 / 15 692× 1.99e-14 1.20e-11 ✓ sig.
superoxide anion generation
CYBA, CYBB, NCF1, NCF2, NCF4
 GO:0042554 5 / 26 399× 4.35e-13 2.04e-10 ✓ sig.
superoxide metabolic process
CYBA, CYBB, NCF1, NCF2
 GO:0006801 4 / 22 378× 1.81e-10 4.81e-8 ✓ sig.
hydrogen peroxide biosynthetic process
CYBA, CYBB, NCF1
 GO:0050665 3 / 11 566× 1.27e-8 2.03e-6 ✓ sig.
cellular response to L-glutamine
CYBA, CYBB
 GO:1904845 2 / 4 1,038× 1.24e-6 9.54e-5 ✓ sig.
innate immune response
CYBA, CYBB, CYBC1, NCF1, NCF2
 GO:0045087 5 / 605 17.2× 3.96e-6 2.45e-4 ✓ sig.
response to aldosterone
CYBA, CYBB
 GO:1904044 2 / 10 415× 9.26e-6 4.78e-4 ✓ sig.
positive regulation of tumor necrosis factor production
CYBA, CYBB, IFNG
 GO:0032760 3 / 113 55.1× 1.76e-5 7.88e-4 ✓ sig.
reactive oxygen species metabolic process
CYBA, NCF1
 GO:0072593 2 / 45 92.3× 2.02e-4 4.85e-3 ✓ sig.
cellular defense response
NCF1, NCF2
 GO:0006968 2 / 51 81.4× 2.60e-4 5.80e-3 ✓ sig.
positive regulation of phagocytosis
CYBA, IFNG
 GO:0050766 2 / 58 71.6× 3.36e-4 6.94e-3 ✓ sig.
ribose phosphate biosynthetic process
G6PD
 GO:0046390 1 / 1 2,076× 4.82e-4 8.81e-3 ✓ sig.
positive regulation of fructose 1,6-bisphosphate metabolic process
IFNG
 GO:0060552 1 / 1 2,076× 4.82e-4 8.81e-3 ✓ sig.
negative regulation of glomerular filtration by angiotensin
CYBA
 GO:0003106 1 / 1 2,076× 4.82e-4 8.81e-3 ✓ sig.
smooth muscle hypertrophy
CYBA
 GO:0014895 1 / 1 2,076× 4.82e-4 8.81e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
G6PD deficiency Hemolytic anemia, g6pd deficient (favism) 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Hemolytic anemia, g6pd deficient (favism) Infections 0.500 1 6.46e-5 1.99e-4 ✓ sig.
G6PD deficiency Infections 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, congenital, non-spherocytic hemolytic, 1 G6PD deficiency 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, nonspherocytic hemolytic Infections 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, nonspherocytic hemolytic Hemolytic anemia, g6pd deficient (favism) 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, nonspherocytic hemolytic G6PD deficiency 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, congenital, non-spherocytic hemolytic, 1 Infections 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, congenital, non-spherocytic hemolytic, 1 Hemolytic anemia, g6pd deficient (favism) 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Anemia, congenital, non-spherocytic hemolytic, 1 Anemia, nonspherocytic hemolytic 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Chronic granulomatous disease, x-linked Granulomatous disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
G6PD deficiency Granulomatous disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Anemia, nonspherocytic hemolytic Granulomatous disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Granulomatous disease Hemolytic anemia, g6pd deficient (favism) 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Granulomatous disease Infections 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Granulomatous disease Granulomatous disease, chronic, autosomal recessive, 5 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Granulomatous disease Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type iii 0.100 1 5.81e-4 1.00e-3 ✓ sig.