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 369

5 diseases · 6 shared-gene connections
5 Diseases
32 Unique genes
0.143 Avg. similarity score
Selective immunoglobulin a deficiency Most-connected disease (4 links)
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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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Selective immunoglobulin a deficiency 4 4 3
Selective iga deficiency disease 3 3 31
Microscopic colitis 2 2 2
joubert syndrome 3 2 2 1
IFIH1-related type 1 interferonopathy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
AHI1 3 / 5 joubert syndrome 3, Selective iga deficiency disease, Selective immunoglobulin a deficiency
CLEC16A 3 / 5 Microscopic colitis, Selective iga deficiency disease, Selective immunoglobulin a deficiency
IFIH1 3 / 5 IFIH1-related type 1 interferonopathy, Selective iga deficiency disease, Selective immunoglobulin a 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 ⇵
Allograft rejection
CD86, FAS, HLA-DQA1, IL2
 KEGG 4 / 39 38.5× 3.20e-6 1.31e-4 ✓ sig.
Type I diabetes mellitus
CD86, FAS, HLA-DQA1, IL2
 KEGG 4 / 44 34.1× 5.23e-6 1.97e-4 ✓ sig.
Graft-versus-host disease
CD86, FAS, HLA-DQA1, IL2
 KEGG 4 / 45 33.4× 5.73e-6 2.12e-4 ✓ sig.
Autoimmune thyroid disease
CD86, FAS, HLA-DQA1, IL2
 KEGG 4 / 54 27.8× 1.20e-5 3.89e-4 ✓ sig.
Inflammatory bowel disease
GATA3, HLA-DQA1, IL2, IL21
 KEGG 4 / 66 22.7× 2.66e-5 7.54e-4 ✓ sig.
Th17 cell differentiation
GATA3, HLA-DQA1, IL2, IL21
 KEGG 4 / 109 13.8× 1.90e-4 3.76e-3 ✓ sig.
Intestinal immune network for IgA production
CD86, HLA-DQA1, IL2
 KEGG 3 / 50 22.5× 3.09e-4 5.50e-3 ✓ sig.
Hepatitis B
IFIH1, CREB3L1, EGR2, FAS
 KEGG 4 / 163 9.2× 8.74e-4 1.22e-2 ✓ sig.
Th1 and Th2 cell differentiation
GATA3, HLA-DQA1, IL2
 KEGG 3 / 93 12.1× 1.89e-3 2.19e-2 ✓ sig.
Human T-cell leukemia virus 1 infection
CREB3L1, EGR2, HLA-DQA1, IL2
 KEGG 4 / 224 6.7× 2.81e-3 2.94e-2 ✓ sig.
Measles
IFIH1, FAS, IL2
 KEGG 3 / 139 8.1× 5.89e-3 4.88e-2 ✓ sig.
cGMP-PKG signaling pathway
CREB3L1, PPIF, PRKG1
 KEGG 3 / 166 6.8× 9.59e-3 6.69e-2
JAK-STAT signaling pathway
IL2, IL21, PTPN2
 KEGG 3 / 168 6.7× 9.90e-3 6.82e-2
Virion - Adenovirus
CD86
 KEGG 1 / 4 93.8× 1.06e-2 7.12e-2
Regulation of glycolysis by fructose 2,6-bisphosphate metabolism
PFKFB3
 Reactome 1 / 4 93.8× 1.06e-2 7.12e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
T cell differentiation
GATA3, IKZF3, IL2, PTPN2
 GO:0030217 4 / 54 43.3× 2.11e-6 1.50e-4 ✓ sig.
positive regulation of immunoglobulin production
CD86, IL2, IL21
 GO:0002639 3 / 33 53.1× 2.40e-5 1.03e-3 ✓ sig.
immune response
MICB, CD86, FAS, FCRL3, HLA-DQA1, IL2, IL21
 GO:0006955 7 / 543 7.5× 3.01e-5 1.22e-3 ✓ sig.
positive regulation of tissue remodeling
IL2, IL21
 GO:0034105 2 / 6 195× 4.24e-5 1.59e-3 ✓ sig.
positive regulation of B cell proliferation
FCRL3, IL2, IL21
 GO:0030890 3 / 47 37.3× 7.03e-5 2.33e-3 ✓ sig.
otic vesicle development
AHI1, GATA3
 GO:0071599 2 / 8 146× 7.90e-5 2.54e-3 ✓ sig.
regulation of B cell differentiation
FCRL3, IKZF3
 GO:0045577 2 / 11 106× 1.55e-4 4.19e-3 ✓ sig.
negative regulation of B cell apoptotic process
FOXP1, IL2
 GO:0002903 2 / 11 106× 1.55e-4 4.19e-3 ✓ sig.
T follicular helper cell differentiation
FOXP1, IL21
 GO:0061470 2 / 11 106× 1.55e-4 4.19e-3 ✓ sig.
positive regulation of T cell proliferation
CD86, IL2, IL21
 GO:0042102 3 / 67 26.1× 2.03e-4 5.10e-3 ✓ sig.
positive regulation of interleukin-4 production
CD86, GATA3
 GO:0032753 2 / 27 43.3× 9.71e-4 1.47e-2 ✓ sig.
positive regulation of interleukin-17 production
IL2, IL21
 GO:0032740 2 / 27 43.3× 9.71e-4 1.47e-2 ✓ sig.
negative regulation of T cell receptor signaling pathway
DGKZ, PTPN2
 GO:0050860 2 / 30 38.9× 1.20e-3 1.69e-2 ✓ sig.
response to virus
IFIH1, GATA3, IL21
 GO:0009615 3 / 128 13.7× 1.35e-3 1.80e-2 ✓ sig.
cochlea development
CDH23, GATA3
 GO:0090102 2 / 35 33.4× 1.63e-3 2.01e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Selective iga deficiency disease Selective immunoglobulin a deficiency 0.094 3 7.39e-9 6.50e-8 ✓ sig.
IFIH1-related type 1 interferonopathy Selective immunoglobulin a deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
joubert syndrome 3 Selective immunoglobulin a deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Microscopic colitis Selective immunoglobulin a deficiency 0.200 1 3.90e-4 8.52e-4 ✓ sig.
joubert syndrome 3 Selective iga deficiency disease 0.031 1 2.01e-3 2.89e-3 ✓ sig.
Microscopic colitis Selective iga deficiency disease 0.030 1 4.02e-3 5.08e-3 ✓ sig.