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 584

5 diseases · 9 shared-gene connections
5 Diseases
11 Unique genes
0.281 Avg. similarity score
Oropharyngeal dysphagia 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 ⇵
Oropharyngeal dysphagia 4 4 1
X-linked non progressive cerebellar ataxia 4 4 1
X-linked progressive cerebellar ataxia 4 4 2
Benign ovarian mucinous tumor 3 3 9
Spinocerebellar ataxia, x-linked 3 3 3

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

Gene ⇵ Member diseases ⇵ Linked diseases
ATP2B3 5 / 5 Benign ovarian mucinous tumor, Oropharyngeal dysphagia, Spinocerebellar ataxia, x-linked, X-linked non progressive cerebellar ataxia and 1 more
GJB1 2 / 5 Spinocerebellar ataxia, x-linked, X-linked progressive cerebellar ataxia
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 ⇵
Endocrine resistance
TP53, CDKN2A, KRAS, GNAS
 KEGG 4 / 99 44.1× 1.37e-6 5.49e-5 ✓ sig.
Bladder cancer
TP53, CDKN2A, KRAS
 KEGG 3 / 41 79.9× 5.98e-6 1.91e-4 ✓ sig.
Cellular senescence
TP53, CDKN2A, RRAS2, KRAS
 KEGG 4 / 157 27.8× 8.64e-6 2.59e-4 ✓ sig.
Hepatocellular carcinoma
TP53, ARID1A, CDKN2A, KRAS
 KEGG 4 / 170 25.7× 1.18e-5 3.35e-4 ✓ sig.
Proteoglycans in cancer
TP53, ANK1, RRAS2, KRAS
 KEGG 4 / 204 21.4× 2.43e-5 6.12e-4 ✓ sig.
Melanoma
TP53, CDKN2A, KRAS
 KEGG 3 / 73 44.9× 3.43e-5 8.10e-4 ✓ sig.
Non-small cell lung cancer
TP53, CDKN2A, KRAS
 KEGG 3 / 73 44.9× 3.43e-5 8.10e-4 ✓ sig.
Human cytomegalovirus infection
TP53, CDKN2A, KRAS, GNAS
 KEGG 4 / 226 19.3× 3.63e-5 8.46e-4 ✓ sig.
Glioma
TP53, CDKN2A, KRAS
 KEGG 3 / 76 43.1× 3.87e-5 8.92e-4 ✓ sig.
Pancreatic cancer
TP53, CDKN2A, KRAS
 KEGG 3 / 77 42.5× 4.03e-5 9.20e-4 ✓ sig.
Chronic myeloid leukemia
TP53, CDKN2A, KRAS
 KEGG 3 / 77 42.5× 4.03e-5 9.20e-4 ✓ sig.
Stabilization of p53
TP53, CDKN2A
 Reactome 2 / 11 199× 4.18e-5 9.47e-4 ✓ sig.
Longevity regulating pathway
TP53, IRS4, KRAS
 KEGG 3 / 90 36.4× 6.43e-5 1.33e-3 ✓ sig.
Mitophagy - animal
TP53, RRAS2, KRAS
 KEGG 3 / 105 31.2× 1.02e-4 1.92e-3 ✓ sig.
SUMOylation of transcription factors
TP53, CDKN2A
 Reactome 2 / 18 121× 1.16e-4 2.13e-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 ⇵
Ras protein signal transduction
TP53, CDKN2A, RRAS2, KRAS
 GO:0007265 4 / 79 86.0× 9.54e-8 1.22e-5 ✓ sig.
rRNA transcription
TP53, CDKN2A
 GO:0009303 2 / 15 227× 3.29e-5 1.35e-3 ✓ sig.
replicative senescence
TP53, CDKN2A
 GO:0090399 2 / 16 212× 3.76e-5 1.49e-3 ✓ sig.
glial cell proliferation
TP53, KRAS
 GO:0014009 2 / 18 189× 4.80e-5 1.79e-3 ✓ sig.
positive regulation of cellular senescence
TP53, KRAS
 GO:2000774 2 / 20 170× 5.95e-5 2.10e-3 ✓ sig.
transcription initiation-coupled chromatin remodeling
TP53, ARID1A
 GO:0045815 2 / 41 82.9× 2.55e-4 6.04e-3 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
ARID1A, CDKN2A
 GO:2000045 2 / 57 59.6× 4.94e-4 9.41e-3 ✓ sig.
cellular senescence
TP53, CDKN2A
 GO:0090398 2 / 57 59.6× 4.94e-4 9.41e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
iron-sulfur cluster export from the mitochondrion
ABCB7
 GO:0140466 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
positive regulation of iron-sulfur cluster assembly
ABCB7
 GO:1903331 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
response to mineralocorticoid
KRAS
 GO:0051385 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
female pregnancy
KRAS, GNAS
 GO:0007565 2 / 80 42.5× 9.71e-4 1.43e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Spinocerebellar ataxia, x-linked X-linked progressive cerebellar ataxia 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Oropharyngeal dysphagia X-linked non progressive cerebellar ataxia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Oropharyngeal dysphagia X-linked progressive cerebellar ataxia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
X-linked non progressive cerebellar ataxia X-linked progressive cerebellar ataxia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Oropharyngeal dysphagia Spinocerebellar ataxia, x-linked 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Spinocerebellar ataxia, x-linked X-linked non progressive cerebellar ataxia 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Benign ovarian mucinous tumor Oropharyngeal dysphagia 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Benign ovarian mucinous tumor X-linked non progressive cerebellar ataxia 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Benign ovarian mucinous tumor X-linked progressive cerebellar ataxia 0.111 1 9.04e-4 1.41e-3 ✓ sig.