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 542

5 diseases · 10 shared-gene connections
5 Diseases
1 Unique genes
0.500 Avg. similarity score
Amyloidosis, hereditary systemic 6 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 ⇵
Amyloidosis, hereditary systemic 6 4 4 1
Beta2-microglobulinic amyloidosis 4 4 1
Hypergammaglobulinemia 4 4 1
Hypoproteinemia, hypercatabolic 4 4 1
Immunodeficiency by defective expression of hla class 1 4 4 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
B2M 5 / 5 Amyloidosis, hereditary systemic 6, Beta2-microglobulinic amyloidosis, Hypergammaglobulinemia, Hypoproteinemia, hypercatabolic and 1 more
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 ⇵
Modulation by Mtb of host immune system
B2M
 Reactome 1 / 7 1,716× 5.83e-4 7.52e-3 ✓ sig.
Endosomal/Vacuolar pathway
B2M
 Reactome 1 / 8 1,501× 6.66e-4 8.31e-3 ✓ sig.
Nef mediated downregulation of MHC class I complex cell surface expression
B2M
 Reactome 1 / 10 1,201× 8.33e-4 9.85e-3 ✓ sig.
DAP12 interactions
B2M
 Reactome 1 / 21 572× 1.75e-3 1.73e-2 ✓ sig.
Antigen Presentation: Folding, assembly and peptide loading of class I MHC
B2M
 Reactome 1 / 25 480× 2.08e-3 1.96e-2 ✓ sig.
DAP12 signaling
B2M
 Reactome 1 / 30 400× 2.50e-3 2.23e-2 ✓ sig.
ER-Phagosome pathway
B2M
 Reactome 1 / 30 400× 2.50e-3 2.23e-2 ✓ sig.
Antigen processing and presentation
B2M
 KEGG 1 / 81 148× 6.74e-3 4.43e-2 ✓ sig.
Interferon gamma signaling
B2M
 Reactome 1 / 87 138× 7.24e-3 4.65e-2 ✓ sig.
Amyloid fiber formation
B2M
 Reactome 1 / 109 110× 9.08e-3 5.36e-2
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
B2M
 Reactome 1 / 130 92.4× 1.08e-2 5.98e-2
Herpes simplex virus 1 infection
B2M
 KEGG 1 / 182 66.0× 1.52e-2 7.30e-2
Epstein-Barr virus infection
B2M
 KEGG 1 / 204 58.9× 1.70e-2 7.81e-2
Human immunodeficiency virus 1 infection
B2M
 KEGG 1 / 213 56.4× 1.77e-2 8.01e-2
Human T-cell leukemia virus 1 infection
B2M
 KEGG 1 / 224 53.6× 1.87e-2 8.23e-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 ⇵
negative regulation of iron ion transport
B2M
 GO:0034757 1 / 1 18,687× 5.35e-5 1.94e-3 ✓ sig.
antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
B2M
 GO:0002481 1 / 2 9,344× 1.07e-4 3.25e-3 ✓ sig.
regulation of iron ion transport
B2M
 GO:0034756 1 / 2 9,344× 1.07e-4 3.25e-3 ✓ sig.
cellular response to iron(III) ion
B2M
 GO:0071283 1 / 2 9,344× 1.07e-4 3.25e-3 ✓ sig.
negative regulation of forebrain neuron differentiation
B2M
 GO:2000978 1 / 2 9,344× 1.07e-4 3.25e-3 ✓ sig.
regulation of erythrocyte differentiation
B2M
 GO:0045646 1 / 6 3,115× 3.21e-4 7.04e-3 ✓ sig.
cellular response to iron ion
B2M
 GO:0071281 1 / 7 2,670× 3.75e-4 7.81e-3 ✓ sig.
cellular response to nicotine
B2M
 GO:0071316 1 / 8 2,336× 4.28e-4 8.53e-3 ✓ sig.
response to molecule of bacterial origin
B2M
 GO:0002237 1 / 9 2,076× 4.82e-4 9.24e-3 ✓ sig.
peptide antigen assembly with MHC class I protein complex
B2M
 GO:0002502 1 / 9 2,076× 4.82e-4 9.24e-3 ✓ sig.
antigen processing and presentation of endogenous peptide antigen via MHC class I
B2M
 GO:0019885 1 / 9 2,076× 4.82e-4 9.24e-3 ✓ sig.
negative regulation of receptor-mediated endocytosis
B2M
 GO:0048261 1 / 10 1,869× 5.35e-4 9.88e-3 ✓ sig.
regulation of membrane depolarization
B2M
 GO:0003254 1 / 10 1,869× 5.35e-4 9.88e-3 ✓ sig.
transferrin transport
B2M
 GO:0033572 1 / 11 1,699× 5.89e-4 1.06e-2 ✓ sig.
positive regulation of T cell cytokine production
B2M
 GO:0002726 1 / 14 1,335× 7.49e-4 1.23e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Amyloidosis, hereditary systemic 6 Beta2-microglobulinic amyloidosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amyloidosis, hereditary systemic 6 Hypergammaglobulinemia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amyloidosis, hereditary systemic 6 Hypoproteinemia, hypercatabolic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Amyloidosis, hereditary systemic 6 Immunodeficiency by defective expression of hla class 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Beta2-microglobulinic amyloidosis Hypergammaglobulinemia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Beta2-microglobulinic amyloidosis Hypoproteinemia, hypercatabolic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Beta2-microglobulinic amyloidosis Immunodeficiency by defective expression of hla class 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypergammaglobulinemia Hypoproteinemia, hypercatabolic 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypergammaglobulinemia Immunodeficiency by defective expression of hla class 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hypoproteinemia, hypercatabolic Immunodeficiency by defective expression of hla class 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.