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 105

12 diseases · 24 shared-gene connections
12 Diseases
24 Unique genes
0.196 Avg. similarity score
Malt lymphoma Most-connected disease (7 links)
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Disease Searched: Pyogenic bacterial infections, recurrent 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 ⇵
Malt lymphoma 7 7 9
Mucosa-associated lymphoma 6 6 4
Splenic diffuse red pulp small b-cell lymphoma 6 6 2
Pyogenic bacterial infections, recurrent 5 5 1
Hajdu-cheney syndrome 4 4 1
Radiologic finding 4 4 10
Waldenstrom macroglobulinemia 4 4 4
Alagille syndrome 3 3 2
Autoinflammatory syndrome, familial, behcet-like 3 3 1
Follicular cyst 3 3 2
Immunodeficiency 37 2 2 1
Abnormality of brain morphology 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
MYD88 6 / 12 Malt lymphoma, Mucosa-associated lymphoma, Pyogenic bacterial infections, recurrent, Radiologic finding and 2 more
NOTCH2 5 / 12 Alagille syndrome, Follicular cyst, Hajdu-cheney syndrome, Malt lymphoma and 1 more
TNFAIP3 4 / 12 Autoinflammatory syndrome, familial, behcet-like, Malt lymphoma, Mucosa-associated lymphoma, Radiologic finding
BCL10 3 / 12 Immunodeficiency 37, Malt lymphoma, Mucosa-associated lymphoma
EXOC2 2 / 12 Abnormality of brain morphology, Waldenstrom macroglobulinemia
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 ⇵
NF-kappa B signaling pathway
TNFAIP3, BCL10, BIRC3, MALT1, MYD88, CARD11
 KEGG 6 / 105 28.6× 4.58e-8 2.82e-6 ✓ sig.
Regulation of TP53 Expression
PRDM1, TP53
 Reactome 2 / 2 500× 3.83e-6 1.31e-4 ✓ sig.
Regulation of TP53 Activity through Methylation
EP300, CHEK2, TP53
 Reactome 3 / 19 79.0× 6.65e-6 2.08e-4 ✓ sig.
Pre-NOTCH Transcription and Translation
NOTCH2, EP300, TP53
 Reactome 3 / 31 48.4× 3.04e-5 7.32e-4 ✓ sig.
Human papillomavirus infection
NOTCH2, JAG1, FAS, EP300, TP53, FOXO1
 KEGG 6 / 333 9.0× 3.83e-5 8.84e-4 ✓ sig.
Pathways in cancer
NOTCH2, JAG1, BIRC3, FAS, EP300, TP53, FOXO1
 KEGG 7 / 533 6.6× 5.83e-5 1.23e-3 ✓ sig.
Regulation of FOXO transcriptional activity by acetylation
EP300, FOXO1
 Reactome 2 / 7 143× 7.99e-5 1.58e-3 ✓ sig.
TNF signaling pathway
JAG1, TNFAIP3, BIRC3, FAS
 KEGG 4 / 119 16.8× 8.35e-5 1.65e-3 ✓ sig.
Thyroid hormone signaling pathway
NOTCH2, EP300, TP53, FOXO1
 KEGG 4 / 122 16.4× 9.20e-5 1.78e-3 ✓ sig.
Shigellosis
BCL10, MALT1, MYD88, TP53, FOXO1
 KEGG 5 / 250 10.0× 1.15e-4 2.12e-3 ✓ sig.
PI5P Regulates TP53 Acetylation
EP300, TP53
 Reactome 2 / 9 111× 1.37e-4 2.43e-3 ✓ sig.
Measles
TNFAIP3, MYD88, FAS, TP53
 KEGG 4 / 139 14.4× 1.53e-4 2.65e-3 ✓ sig.
Constitutive Signaling by NOTCH1 PEST Domain Mutants
JAG1, EP300, TBL1XR1
 Reactome 3 / 58 25.9× 2.01e-4 3.30e-3 ✓ sig.
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
JAG1, EP300, TBL1XR1
 Reactome 3 / 58 25.9× 2.01e-4 3.30e-3 ✓ sig.
Stabilization of p53
CHEK2, TP53
 Reactome 2 / 11 91.0× 2.08e-4 3.39e-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 ⇵
apoptotic process
NOTCH2, TNFAIP3, BCL10, BIRC3, MYD88, FAS, EP300, CHEK2, TP53, FOXO1
 GO:0006915 10 / 747 10.4× 1.16e-8 2.00e-6 ✓ sig.
regulation of apoptotic process
NOTCH2, BCL10, BIRC3, MALT1, FAS, CARD11, TP53
 GO:0042981 7 / 254 21.5× 2.24e-8 3.56e-6 ✓ sig.
lipopolysaccharide-mediated signaling pathway
SCARB1, BCL10, MALT1, MYD88
 GO:0031663 4 / 38 82.0× 1.50e-7 1.79e-5 ✓ sig.
regulation of cell population proliferation
JAG1, TNFAIP3, MYD88, PRDM1, TP53, FOXO1
 GO:0042127 6 / 201 23.2× 1.65e-7 1.93e-5 ✓ sig.
cardiac septum morphogenesis
NOTCH2, JAG1, TP53
 GO:0060411 3 / 16 146× 1.03e-6 8.79e-5 ✓ sig.
regulation of chemokine (C-X-C motif) ligand 2 production
FOXP1, MYD88
 GO:2000341 2 / 4 389× 9.47e-6 5.21e-4 ✓ sig.
ciliary body morphogenesis
NOTCH2, JAG1
 GO:0061073 2 / 4 389× 9.47e-6 5.21e-4 ✓ sig.
positive regulation of canonical NF-kappaB signal transduction
BCL10, BIRC3, MALT1, MYD88, CARD11
 GO:0043123 5 / 232 16.8× 9.90e-6 5.40e-4 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
EP300, CHEK2, TP53
 GO:0042771 3 / 33 70.8× 9.90e-6 5.40e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
NOTCH2, JAG1, IRF4, MYD88, EP300, TBL1XR1, TP53, FOXO1, KMT2D
 GO:0045944 9 / 1,208 5.8× 1.03e-5 5.56e-4 ✓ sig.
non-canonical NF-kappaB signal transduction
BCL10, BIRC3, MYD88
 GO:0038061 3 / 34 68.7× 1.09e-5 5.79e-4 ✓ sig.
multicellular organism growth
NOTCH2, EP300, TBL1XR1, TP53
 GO:0035264 4 / 115 27.1× 1.32e-5 6.72e-4 ✓ sig.
positive regulation of interleukin-2 production
MALT1, IRF4, CARD11
 GO:0032743 3 / 37 63.1× 1.41e-5 7.09e-4 ✓ sig.
cellular response to hyperoxia
FAS, FOXO1
 GO:0071455 2 / 5 311× 1.58e-5 7.74e-4 ✓ sig.
response to fungus
BCL10, MALT1
 GO:0009620 2 / 6 260× 2.36e-5 1.05e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Malt lymphoma Mucosa-associated lymphoma 0.273 3 5.43e-10 4.80e-9 ✓ sig.
Malt lymphoma Splenic diffuse red pulp small b-cell lymphoma 0.200 2 3.00e-7 1.96e-6 ✓ sig.
Mucosa-associated lymphoma Radiologic finding 0.167 2 1.80e-6 1.06e-5 ✓ sig.
Malt lymphoma Radiologic finding 0.118 2 1.08e-5 5.82e-5 ✓ sig.
Alagille syndrome Hajdu-cheney syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pyogenic bacterial infections, recurrent Splenic diffuse red pulp small b-cell lymphoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hajdu-cheney syndrome Splenic diffuse red pulp small b-cell lymphoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Follicular cyst Hajdu-cheney syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Alagille syndrome Splenic diffuse red pulp small b-cell lymphoma 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Alagille syndrome Follicular cyst 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Follicular cyst Splenic diffuse red pulp small b-cell lymphoma 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Mucosa-associated lymphoma Pyogenic bacterial infections, recurrent 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Pyogenic bacterial infections, recurrent Waldenstrom macroglobulinemia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Autoinflammatory syndrome, familial, behcet-like Mucosa-associated lymphoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Immunodeficiency 37 Mucosa-associated lymphoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Abnormality of brain morphology Waldenstrom macroglobulinemia 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Splenic diffuse red pulp small b-cell lymphoma Waldenstrom macroglobulinemia 0.167 1 5.16e-4 9.13e-4 ✓ sig.
Hajdu-cheney syndrome Malt lymphoma 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Autoinflammatory syndrome, familial, behcet-like Malt lymphoma 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Autoinflammatory syndrome, familial, behcet-like Radiologic finding 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Immunodeficiency 37 Malt lymphoma 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Malt lymphoma Pyogenic bacterial infections, recurrent 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Pyogenic bacterial infections, recurrent Radiologic finding 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Mucosa-associated lymphoma Waldenstrom macroglobulinemia 0.125 1 1.03e-3 1.57e-3 ✓ sig.