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 77

14 diseases · 32 shared-gene connections
14 Diseases
19 Unique genes
0.298 Avg. similarity score
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly Most-connected disease (8 links)
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Disease Searched: Imagawa-matsumoto syndrome 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 ⇵
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly 8 8 2
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant 7 7 1
Benta disease 7 7 1
Immunodeficiency 11a, autosomal recessive 7 7 1
Immunodeficiency 11b with atopic dermatitis 7 7 1
B-cell expansion with nfkb and t-cell anergy 6 6 1
Congenital cardiovascular anomaly 5 5 7
Osteopenia 5 5 6
Weaver syndrome 4 4 5
Upper extremity deformity, congenital 3 3 1
Lymphoma, aids-related 2 2 3
Cohen-gibson syndrome 1 1 1
Fanconi anemia complementation group C 1 1 2
Imagawa-matsumoto syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CARD11 8 / 14 B cell expansion with nfkb and t cell anergy (benta), autosomal dominant, B-cell expansion with nfkb and t-cell anergy, Benta disease, Congenital cardiovascular anomaly and 4 more
EZH2 4 / 14 Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly, Lymphoma, aids-related, Upper extremity deformity, congenital, Weaver syndrome
EED 2 / 14 Cohen-gibson syndrome, Weaver syndrome
FANCC 2 / 14 Congenital cardiovascular anomaly, Fanconi anemia complementation group C
NSD1 2 / 14 Osteopenia, Weaver syndrome
SUZ12 2 / 14 Imagawa-matsumoto syndrome, Weaver syndrome
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 ⇵
PKMTs methylate histone lysines
EED, NSD1, EZH2, SUZ12
 Reactome 4 / 71 35.6× 4.06e-6 1.38e-4 ✓ sig.
Transcriptional Regulation by E2F6
EED, EZH2, SUZ12
 Reactome 3 / 35 54.2× 2.13e-5 5.48e-4 ✓ sig.
Regulation of PTEN gene transcription
EED, EZH2, SUZ12
 Reactome 3 / 53 35.8× 7.48e-5 1.50e-3 ✓ sig.
PRC2 methylates histones and DNA
EED, EZH2, SUZ12
 Reactome 3 / 73 26.0× 1.95e-4 3.21e-3 ✓ sig.
Proteoglycans in cancer
ANK2, COL1A1, PIK3CA, MYC
 KEGG 4 / 204 12.4× 2.56e-4 3.99e-3 ✓ sig.
Polycomb repressive complex
EED, EZH2, SUZ12
 KEGG 3 / 83 22.8× 2.85e-4 4.33e-3 ✓ sig.
Oxidative Stress Induced Senescence
EED, EZH2, SUZ12
 Reactome 3 / 125 15.2× 9.44e-4 1.09e-2 ✓ sig.
HCMV Early Events
EED, EZH2, SUZ12
 Reactome 3 / 135 14.0× 1.18e-3 1.28e-2 ✓ sig.
GPVI-mediated activation cascade
COL1A1, PIK3CA
 Reactome 2 / 34 37.2× 1.29e-3 1.38e-2 ✓ sig.
Breast cancer
LRP5, PIK3CA, MYC
 KEGG 3 / 148 12.8× 1.54e-3 1.57e-2 ✓ sig.
Gastric cancer
LRP5, PIK3CA, MYC
 KEGG 3 / 150 12.6× 1.60e-3 1.61e-2 ✓ sig.
Hepatocellular carcinoma
LRP5, PIK3CA, MYC
 KEGG 3 / 170 11.2× 2.29e-3 2.10e-2 ✓ sig.
Epstein-Barr virus infection
PIK3CA, TNFAIP3, MYC
 KEGG 3 / 204 9.3× 3.83e-3 3.03e-2 ✓ sig.
Endometrial cancer
PIK3CA, MYC
 KEGG 2 / 59 21.4× 3.84e-3 3.04e-2 ✓ sig.
Lysine degradation
NSD1, EZH2
 KEGG 2 / 63 20.1× 4.37e-3 3.33e-2 ✓ 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 ⇵
facultative heterochromatin formation
EED, EZH2, SUZ12
 GO:0140718 3 / 7 422× 3.11e-8 4.74e-6 ✓ sig.
positive regulation of mesenchymal cell proliferation
LRP5, MYC
 GO:0002053 2 / 26 75.7× 3.14e-4 7.00e-3 ✓ sig.
vasculature development
LRP5, PIK3CA
 GO:0001944 2 / 33 59.6× 5.08e-4 9.59e-3 ✓ sig.
skeletal system morphogenesis
COL1A1, MYC
 GO:0048705 2 / 45 43.7× 9.45e-4 1.42e-2 ✓ sig.
oligodendrocyte differentiation
EED, SUZ12
 GO:0048709 2 / 45 43.7× 9.45e-4 1.42e-2 ✓ sig.
chromatin organization
EED, NSD1, EZH2, SUZ12
 GO:0006325 4 / 449 8.8× 9.57e-4 1.42e-2 ✓ sig.
adipose tissue development
LRP5, PIK3CA
 GO:0060612 2 / 46 42.8× 9.87e-4 1.45e-2 ✓ sig.
protein localization to T-tubule
ANK2
 GO:0036371 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
atrial cardiac muscle cell to AV node cell communication
ANK2
 GO:0086066 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
SA node cell to atrial cardiac muscle cell communication
ANK2
 GO:0086070 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
cellular response to vitamin E
COL1A1
 GO:0071306 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
negative regulation of toll-like receptor 5 signaling pathway
TNFAIP3
 GO:0034148 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
regulation of vascular wound healing
TNFAIP3
 GO:0061043 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway
TNFAIP3
 GO:0070429 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.
establishment of protein localization to vacuole
TNFAIP3
 GO:0072666 1 / 1 984× 1.02e-3 1.48e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant Immunodeficiency 11b with atopic dermatitis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant Benta disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Immunodeficiency 11a, autosomal recessive Immunodeficiency 11b with atopic dermatitis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Benta disease Immunodeficiency 11a, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Benta disease Immunodeficiency 11b with atopic dermatitis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B-cell expansion with nfkb and t-cell anergy Immunodeficiency 11a, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B-cell expansion with nfkb and t-cell anergy Immunodeficiency 11b with atopic dermatitis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B-cell expansion with nfkb and t-cell anergy Benta disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant B-cell expansion with nfkb and t-cell anergy 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant Immunodeficiency 11a, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
B-cell expansion with nfkb and t-cell anergy Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly 0.333 1 1.29e-4 3.27e-4 ✓ sig.
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Benta disease Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly Upper extremity deformity, congenital 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly Immunodeficiency 11b with atopic dermatitis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly Immunodeficiency 11a, autosomal recessive 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Lymphoma, aids-related Upper extremity deformity, congenital 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Imagawa-matsumoto syndrome Weaver syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Upper extremity deformity, congenital Weaver syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cohen-gibson syndrome Weaver syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly Lymphoma, aids-related 0.200 1 3.87e-4 7.33e-4 ✓ sig.
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant Osteopenia 0.143 1 3.87e-4 7.33e-4 ✓ sig.
B-cell expansion with nfkb and t-cell anergy Osteopenia 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Benta disease Osteopenia 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Immunodeficiency 11b with atopic dermatitis Osteopenia 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Immunodeficiency 11a, autosomal recessive Osteopenia 0.143 1 3.87e-4 7.33e-4 ✓ sig.
B cell expansion with nfkb and t cell anergy (benta), autosomal dominant Congenital cardiovascular anomaly 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Congenital cardiovascular anomaly Immunodeficiency 11a, autosomal recessive 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Congenital cardiovascular anomaly Immunodeficiency 11b with atopic dermatitis 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Benta disease Congenital cardiovascular anomaly 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Epstein-barr virus-positive diffuse large b-cell lymphoma of the elderly Weaver syndrome 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Congenital cardiovascular anomaly Fanconi anemia complementation group C 0.111 1 9.04e-4 1.41e-3 ✓ sig.