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 447

6 diseases · 8 shared-gene connections
6 Diseases
7 Unique genes
0.224 Avg. similarity score
Proteasome associated autoinflammatory syndrome Most-connected disease (5 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 ⇵
Proteasome associated autoinflammatory syndrome 5 5 7
Autoinflammation, lipodystrophy, and dermatosis syndrome 3 3 2
Candle syndrome 3 3 2
Nakajo syndrome 3 3 1
Immunodeficiency 121 with autoinflammation 1 1 1
Keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PSMB8 4 / 6 Autoinflammation, lipodystrophy, and dermatosis syndrome, Candle syndrome, Nakajo syndrome, Proteasome associated autoinflammatory syndrome
POMP 2 / 6 Keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome, Proteasome associated autoinflammatory syndrome
PSMB10 2 / 6 Immunodeficiency 121 with autoinflammation, Proteasome associated autoinflammatory syndrome
PSMB4 2 / 6 Candle syndrome, Proteasome associated autoinflammatory syndrome
PSMB9 2 / 6 Autoinflammation, lipodystrophy, and dermatosis syndrome, Proteasome associated autoinflammatory 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 ⇵
Proteasome
PSMB4, PSMB8, POMP, PSMA3, PSMB9, PSMB10
 KEGG 6 / 46 224× 1.57e-14 4.28e-12 ✓ sig.
Cross-presentation of soluble exogenous antigens (endosomes)
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 50 172× 2.13e-11 2.98e-9 ✓ sig.
Ubiquitin-dependent degradation of Cyclin D
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 51 168× 2.36e-11 3.29e-9 ✓ sig.
Regulation of ornithine decarboxylase (ODC)
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 51 168× 2.36e-11 3.29e-9 ✓ sig.
G2/M Checkpoints
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 51 168× 2.36e-11 3.29e-9 ✓ sig.
Vpu mediated degradation of CD4
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 52 165× 2.61e-11 3.61e-9 ✓ sig.
Autodegradation of the E3 ubiquitin ligase COP1
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 52 165× 2.61e-11 3.61e-9 ✓ sig.
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 52 165× 2.61e-11 3.61e-9 ✓ sig.
Vif-mediated degradation of APOBEC3G
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 54 159× 3.17e-11 4.27e-9 ✓ sig.
FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 54 159× 3.17e-11 4.27e-9 ✓ sig.
SCF-beta-TrCP mediated degradation of Emi1
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 55 156× 3.49e-11 4.66e-9 ✓ sig.
Degradation of AXIN
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 55 156× 3.49e-11 4.66e-9 ✓ sig.
Regulation of RUNX3 expression and activity
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 55 156× 3.49e-11 4.66e-9 ✓ sig.
AUF1 (hnRNP D0) binds and destabilizes mRNA
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 56 153× 3.83e-11 5.07e-9 ✓ sig.
Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 Reactome 5 / 56 153× 3.83e-11 5.07e-9 ✓ 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 ⇵
proteolysis involved in protein catabolic process
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 GO:0051603 5 / 53 252× 3.16e-12 1.35e-9 ✓ sig.
proteasome-mediated ubiquitin-dependent protein catabolic process
PSMB4, PSMB8, PSMA3, PSMB9, PSMB10
 GO:0043161 5 / 343 38.9× 4.12e-8 6.02e-6 ✓ sig.
proteasome assembly
POMP, PSMG2
 GO:0043248 2 / 11 485× 6.60e-6 3.94e-4 ✓ sig.
proteolysis
PSMB8, PSMB9, PSMB10
 GO:0006508 3 / 613 13.1× 1.11e-3 1.55e-2 ✓ sig.
chaperone-mediated protein complex assembly
PSMG2
 GO:0051131 1 / 24 111× 8.96e-3 4.41e-2 ✓ sig.
negative regulation of inflammatory response to antigenic stimulus
PSMB4
 GO:0002862 1 / 26 103× 9.70e-3 4.58e-2 ✓ sig.
mitotic spindle assembly checkpoint signaling
PSMG2
 GO:0007094 1 / 30 89.0× 1.12e-2 4.89e-2 ✓ sig.
antigen processing and presentation
PSMB8
 GO:0019882 1 / 48 55.6× 1.78e-2 6.13e-2
T cell proliferation
PSMB10
 GO:0042098 1 / 51 52.3× 1.90e-2 6.34e-2
humoral immune response
PSMB10
 GO:0006959 1 / 58 46.0× 2.15e-2 6.77e-2
fat cell differentiation
PSMB8
 GO:0045444 1 / 93 28.7× 3.43e-2 8.63e-2
cell morphogenesis
PSMB10
 GO:0000902 1 / 119 22.4× 4.37e-2 9.92e-2
immune system process
PSMB8, PSMB9
 GO:0002376 2 / 943 5.7× 4.51e-2 1.01e-1
ubiquitin-dependent protein catabolic process
PSMA3
 GO:0006511 1 / 257 10.4× 9.24e-2 1.57e-1
regulation of cell cycle
PSMG2
 GO:0051726 1 / 262 10.2× 9.41e-2 1.59e-1

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Autoinflammation, lipodystrophy, and dermatosis syndrome Proteasome associated autoinflammatory syndrome 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Candle syndrome Proteasome associated autoinflammatory syndrome 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Autoinflammation, lipodystrophy, and dermatosis syndrome Nakajo syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Candle syndrome Nakajo syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Autoinflammation, lipodystrophy, and dermatosis syndrome Candle syndrome 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Immunodeficiency 121 with autoinflammation Proteasome associated autoinflammatory syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome Proteasome associated autoinflammatory syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Nakajo syndrome Proteasome associated autoinflammatory syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.