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 277

8 diseases · 13 shared-gene connections
8 Diseases
13 Unique genes
0.242 Avg. similarity score
Cleft lip with or without cleft palate Most-connected disease (6 links)
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Disease Searched: Non-syndromic orofacial cleft 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 ⇵
Cleft lip with or without cleft palate 6 6 6
Blepharocheilodontic syndrome 5 5 2
Atypical lobular breast hyperplasia 4 4 2
Hereditary diffuse gastric and lobular breast cancer syndrome 4 4 1
Diffuse gastric and lobular breast cancer syndrome 3 3 2
Trigeminal nerve disease 2 2 6
Bilateral cleft lip 1 1 1
Non-syndromic orofacial cleft 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CDH1 5 / 8 Atypical lobular breast hyperplasia, Blepharocheilodontic syndrome, Cleft lip with or without cleft palate, Diffuse gastric and lobular breast cancer syndrome and 1 more
CTNND1 3 / 8 Blepharocheilodontic syndrome, Cleft lip with or without cleft palate, Trigeminal nerve disease
ARHGAP29 2 / 8 Cleft lip with or without cleft palate, Non-syndromic orofacial cleft
PLEKHA5 2 / 8 Bilateral cleft lip, Cleft lip with or without cleft palate
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 ⇵
Adherens junction
CDH1, CTNND1, ARHGAP29, CTNNA1
 KEGG 4 / 93 39.7× 2.28e-6 8.44e-5 ✓ sig.
Adherens junctions interactions
CDH1, CTNND1, CTNNA1
 Reactome 3 / 32 86.6× 4.83e-6 1.60e-4 ✓ sig.
Endometrial cancer
CDH1, CTNNA1, PIK3CA
 KEGG 3 / 59 47.0× 3.11e-5 7.47e-4 ✓ sig.
InlA-mediated entry of Listeria monocytogenes into host cells
CDH1, CTNND1
 Reactome 2 / 9 205× 3.88e-5 8.92e-4 ✓ sig.
Bacterial invasion of epithelial cells
CDH1, CTNNA1, PIK3CA
 KEGG 3 / 78 35.5× 7.19e-5 1.46e-3 ✓ sig.
Leukocyte transendothelial migration
CTNND1, CTNNA1, PIK3CA
 KEGG 3 / 116 23.9× 2.34e-4 3.71e-3 ✓ sig.
VEGFR2 mediated vascular permeability
CTNND1, CTNNA1
 Reactome 2 / 29 63.7× 4.32e-4 5.96e-3 ✓ sig.
Gastric cancer
CDH1, CTNNA1, PIK3CA
 KEGG 3 / 150 18.5× 4.98e-4 6.67e-3 ✓ sig.
RHO GTPases activate IQGAPs
CDH1, CTNNA1
 Reactome 2 / 32 57.7× 5.27e-4 6.95e-3 ✓ sig.
Synthesis of PIPs at the plasma membrane
PLEKHA5, PIK3CA
 Reactome 2 / 51 36.2× 1.34e-3 1.41e-2 ✓ sig.
Rap1 signaling pathway
CDH1, CTNND1, PIK3CA
 KEGG 3 / 211 13.1× 1.34e-3 1.42e-2 ✓ sig.
Melanoma
CDH1, PIK3CA
 KEGG 2 / 73 25.3× 2.72e-3 2.38e-2 ✓ sig.
MET activates PI3K/AKT signaling
PIK3CA
 Reactome 1 / 6 154× 6.48e-3 4.32e-2 ✓ sig.
IRS-mediated signalling
PIK3CA
 Reactome 1 / 6 154× 6.48e-3 4.32e-2 ✓ sig.
PI3K/AKT activation
PIK3CA
 Reactome 1 / 9 103× 9.70e-3 5.59e-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 ⇵
cell-cell adhesion mediated by cadherin
CDH1, CTNND1, PLEKHA7, DCHS2
 GO:0044331 4 / 42 137× 1.55e-8 2.59e-6 ✓ sig.
cell-cell adhesion
CDH1, CTNND1, PLEKHA7, CTNNA1, DCHS2
 GO:0098609 5 / 218 33.0× 2.46e-7 2.69e-5 ✓ sig.
cellular response to indole-3-methanol
CDH1, CTNNA1
 GO:0071681 2 / 5 575× 4.46e-6 2.89e-4 ✓ sig.
epithelial cell-cell adhesion
PLEKHA7, CTNNA1
 GO:0090136 2 / 12 240× 2.94e-5 1.23e-3 ✓ sig.
establishment or maintenance of cell polarity
CTNNA1, DCHS2
 GO:0007163 2 / 43 66.9× 3.97e-4 8.13e-3 ✓ sig.
negative regulation of blood vessel branching
CTNND1
 GO:1905554 1 / 1 1,437× 6.96e-4 1.18e-2 ✓ sig.
response to butyrate
PIK3CA
 GO:1903544 1 / 1 1,437× 6.96e-4 1.18e-2 ✓ sig.
cell adhesion
CDH1, CTNND1, CTNNA1, DCHS2
 GO:0007155 4 / 665 8.6× 8.79e-4 1.36e-2 ✓ sig.
cell migration
CDH1, CTNNA1, PIK3CA
 GO:0016477 3 / 303 14.2× 1.07e-3 1.51e-2 ✓ sig.
negative regulation of miRNA catabolic process
TENT2
 GO:2000626 1 / 2 719× 1.39e-3 1.75e-2 ✓ sig.
ureteric bud invasion
KIF26B
 GO:0072092 1 / 2 719× 1.39e-3 1.75e-2 ✓ sig.
response to muscle inactivity
PIK3CA
 GO:0014870 1 / 2 719× 1.39e-3 1.75e-2 ✓ sig.
positive regulation of protein localization to cell-cell junction
CTNND1
 GO:0150107 1 / 3 479× 2.09e-3 2.17e-2 ✓ sig.
condensed mesenchymal cell proliferation
DCHS2
 GO:0072137 1 / 3 479× 2.09e-3 2.17e-2 ✓ sig.
cellular response to hydrostatic pressure
PIK3CA
 GO:0071464 1 / 3 479× 2.09e-3 2.17e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Blepharocheilodontic syndrome Cleft lip with or without cleft palate 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Atypical lobular breast hyperplasia Hereditary diffuse gastric and lobular breast cancer syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Atypical lobular breast hyperplasia Blepharocheilodontic syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Atypical lobular breast hyperplasia Diffuse gastric and lobular breast cancer syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Blepharocheilodontic syndrome Hereditary diffuse gastric and lobular breast cancer syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Diffuse gastric and lobular breast cancer syndrome Hereditary diffuse gastric and lobular breast cancer syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Blepharocheilodontic syndrome Diffuse gastric and lobular breast cancer syndrome 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Atypical lobular breast hyperplasia Cleft lip with or without cleft palate 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Bilateral cleft lip Cleft lip with or without cleft palate 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cleft lip with or without cleft palate Hereditary diffuse gastric and lobular breast cancer syndrome 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Cleft lip with or without cleft palate Non-syndromic orofacial cleft 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Blepharocheilodontic syndrome Trigeminal nerve disease 0.125 1 7.75e-4 1.25e-3 ✓ sig.
Cleft lip with or without cleft palate Trigeminal nerve disease 0.083 1 2.32e-3 3.05e-3 ✓ sig.