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 562

5 diseases · 7 shared-gene connections
5 Diseases
28 Unique genes
0.235 Avg. similarity score
Epithelial ovarian carcinoma 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 ⇵
Epithelial ovarian carcinoma 4 4 28
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development 3 3 1
Epileptic encephalopathy, infantile or early childhood, 1 3 3 1
Severe neurodevelopmental disease with seizures 3 3 1
Palmoplantar hyperkeratosis with squamous cell carcinoma of skin and sex reversal 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PPP3CA 4 / 5 Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development, Epileptic encephalopathy, infantile or early childhood, 1, Epithelial ovarian carcinoma, Severe neurodevelopmental disease with seizures
RSPO1 2 / 5 Epithelial ovarian carcinoma, Palmoplantar hyperkeratosis with squamous cell carcinoma of skin and sex reversal
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 ⇵
Chemical carcinogenesis - receptor activation
CYP3A4, FOS, GSTM1, GSTT1, KPNB1, RAF1
 KEGG 6 / 215 12.0× 8.32e-6 2.50e-4 ✓ sig.
Fluid shear stress and atherosclerosis
CAV1, FOS, GSTM1, GSTT1, TP53
 KEGG 5 / 141 15.2× 1.64e-5 4.42e-4 ✓ sig.
Breast cancer
ERBB2, FOS, RAF1, TP53, WNT4
 KEGG 5 / 148 14.5× 2.08e-5 5.38e-4 ✓ sig.
Platinum drug resistance
ERBB2, GSTM1, GSTT1, TP53
 KEGG 4 / 75 22.9× 2.56e-5 6.40e-4 ✓ sig.
Hepatocellular carcinoma
GSTM1, GSTT1, RAF1, TP53, WNT4
 KEGG 5 / 170 12.6× 4.04e-5 9.22e-4 ✓ sig.
Endocrine resistance
ERBB2, FOS, RAF1, TP53
 KEGG 4 / 99 17.3× 7.64e-5 1.53e-3 ✓ sig.
Proteoglycans in cancer
CAV1, ERBB2, RAF1, TP53, WNT4
 KEGG 5 / 204 10.5× 9.62e-5 1.84e-3 ✓ sig.
Bladder cancer
ERBB2, RAF1, TP53
 KEGG 3 / 41 31.4× 1.14e-4 2.10e-3 ✓ sig.
Pathways in cancer
ERBB2, FOS, GSTM1, GSTT1, RAF1, TP53, WNT4
 KEGG 7 / 533 5.6× 1.71e-4 2.91e-3 ✓ sig.
Glutathione metabolism
GPX6, GSTM1, GSTT1
 KEGG 3 / 59 21.8× 3.38e-4 4.94e-3 ✓ sig.
Endometrial cancer
ERBB2, RAF1, TP53
 KEGG 3 / 59 21.8× 3.38e-4 4.94e-3 ✓ sig.
Gastric cancer
ERBB2, RAF1, TP53, WNT4
 KEGG 4 / 150 11.4× 3.79e-4 5.39e-3 ✓ sig.
Chemical carcinogenesis - DNA adducts
CYP3A4, GSTM1, GSTT1
 KEGG 3 / 70 18.4× 5.60e-4 7.29e-3 ✓ sig.
MAPK signaling pathway
PPP3CA, ERBB2, FOS, RAF1, TP53
 KEGG 5 / 299 7.2× 5.68e-4 7.37e-3 ✓ sig.
Prolactin signaling pathway
FOS, RAF1, SOCS7
 KEGG 3 / 71 18.1× 5.83e-4 7.52e-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 ⇵
immature T cell proliferation in thymus
ERBB2, WNT4
 GO:0033080 2 / 5 267× 2.16e-5 9.80e-4 ✓ sig.
positive regulation of DNA metabolic process
AGER, ATAD5
 GO:0051054 2 / 6 222× 3.24e-5 1.33e-3 ✓ sig.
ERBB2-ERBB3 signaling pathway
ERBB2, RAF1
 GO:0038133 2 / 9 148× 7.74e-5 2.56e-3 ✓ sig.
cellular response to transforming growth factor beta stimulus
CAV1, FOS, WNT4
 GO:0071560 3 / 67 29.9× 1.35e-4 3.84e-3 ✓ sig.
wound healing
PPP3CA, ERBB2, RAF1
 GO:0042060 3 / 76 26.3× 1.97e-4 5.02e-3 ✓ sig.
type II interferon-mediated signaling pathway
RAF1, TP53
 GO:0060333 2 / 15 89.0× 2.25e-4 5.51e-3 ✓ sig.
apoptotic signaling pathway
CAV1, TP53, WNT4
 GO:0097190 3 / 84 23.8× 2.65e-4 6.21e-3 ✓ sig.
cellular response to starvation
CAV1, EHMT2, WNT4
 GO:0009267 3 / 90 22.2× 3.24e-4 7.08e-3 ✓ sig.
oocyte development
EHMT2, WNT4
 GO:0048599 2 / 19 70.3× 3.64e-4 7.70e-3 ✓ sig.
Schwann cell development
ERBB2, RAF1
 GO:0014044 2 / 20 66.7× 4.05e-4 8.24e-3 ✓ sig.
response to muscle stretch
FOS, RAF1
 GO:0035994 2 / 20 66.7× 4.05e-4 8.24e-3 ✓ sig.
negative regulation of telomere maintenance via telomerase
STN1, TP53
 GO:0032211 2 / 22 60.7× 4.91e-4 9.37e-3 ✓ sig.
protein import into nucleus
PPP3CA, KPNB1, TP53
 GO:0006606 3 / 110 18.2× 5.84e-4 1.06e-2 ✓ sig.
cell population proliferation
ATAD5, CAV1, ERBB2, TP53
 GO:0008283 4 / 263 10.2× 6.02e-4 1.08e-2 ✓ sig.
positive regulation of activated T cell proliferation
PPP3CA, AGER
 GO:0042104 2 / 28 47.7× 7.99e-4 1.28e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development Severe neurodevelopmental disease with seizures 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development Epileptic encephalopathy, infantile or early childhood, 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epileptic encephalopathy, infantile or early childhood, 1 Severe neurodevelopmental disease with seizures 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development Epithelial ovarian carcinoma 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Epileptic encephalopathy, infantile or early childhood, 1 Epithelial ovarian carcinoma 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Epithelial ovarian carcinoma Palmoplantar hyperkeratosis with squamous cell carcinoma of skin and sex reversal 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Epithelial ovarian carcinoma Severe neurodevelopmental disease with seizures 0.036 1 1.74e-3 2.42e-3 ✓ sig.