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 270

7 diseases · 12 shared-gene connections
7 Diseases
32 Unique genes
0.198 Avg. similarity score
Tongue neoplasms 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 ⇵
Tongue neoplasms 5 5 10
Dermatopathia pigmentosa reticularis 4 4 1
Epidermolysis bullosa simplex 4 4 1
Sjogren-larsson syndrome 4 4 2
Weber-cockayne syndrome 3 3 4
Ductal carcinoma of breast 2 2 12
Papilloma 2 2 12

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

Gene ⇵ Member diseases ⇵ Linked diseases
KRT14 5 / 7 Dermatopathia pigmentosa reticularis, Epidermolysis bullosa simplex, Sjogren-larsson syndrome, Tongue neoplasms and 1 more
PTGS2 3 / 7 Ductal carcinoma of breast, Papilloma, Tongue neoplasms
SOD2 3 / 7 Ductal carcinoma of breast, Papilloma, Tongue neoplasms
ERBB2 2 / 7 Ductal carcinoma of breast, Papilloma
HRAS 2 / 7 Papilloma, Tongue neoplasms
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 ⇵
Gastric cancer
CDH1, ERBB2, SMAD4, CCND1, CDKN1A, EGFR, HRAS, TGFB1, TERT
 KEGG 9 / 150 22.5× 1.28e-10 1.80e-8 ✓ sig.
Pathways in cancer
CDH1, ERBB2, PTGER1, PTGS2, SMAD4, CCND1, CDKN1A, EGFR, HRAS, NQO1, TGFA, TGFB1
 KEGG 13 / 533 9.2× 3.58e-10 4.55e-8 ✓ sig.
Hepatocellular carcinoma
SMAD4, CCND1, CDKN1A, EGFR, HRAS, NQO1, TGFA, TGFB1, TERT
 KEGG 9 / 170 19.9× 3.91e-10 4.88e-8 ✓ sig.
Bladder cancer
CDH1, ERBB2, CCND1, CDKN1A, EGFR, HRAS
 KEGG 6 / 41 54.9× 9.17e-10 1.04e-7 ✓ sig.
Pancreatic cancer
ERBB2, SMAD4, CCND1, CDKN1A, EGFR, TGFA, TGFB1
 KEGG 7 / 77 34.1× 9.98e-10 1.12e-7 ✓ sig.
Colorectal cancer
SMAD4, CCND1, CDKN1A, EGFR, HRAS, TGFA, TGFB1
 KEGG 7 / 87 30.2× 2.38e-9 2.40e-7 ✓ sig.
Prostate cancer
ATF4, ERBB2, CCND1, CDKN1A, EGFR, HRAS, TGFA
 KEGG 7 / 98 26.8× 5.52e-9 5.21e-7 ✓ sig.
Endometrial cancer
CDH1, ERBB2, CCND1, CDKN1A, EGFR, HRAS
 KEGG 6 / 59 38.2× 8.89e-9 7.89e-7 ✓ sig.
Non-small cell lung cancer
ERBB2, CCND1, CDKN1A, EGFR, HRAS, TGFA
 KEGG 6 / 73 30.8× 3.27e-8 2.47e-6 ✓ sig.
FoxO signaling pathway
SMAD4, SOD2, CCND1, CDKN1A, EGFR, HRAS, TGFB1
 KEGG 7 / 133 19.8× 4.66e-8 3.35e-6 ✓ sig.
Human T-cell leukemia virus 1 infection
ATF4, SMAD4, CCND1, CDKN1A, HRAS, TGFB1, HLA-DQB1, TERT
 KEGG 8 / 224 13.4× 9.24e-8 6.12e-6 ✓ sig.
RUNX3 regulates CDKN1A transcription
SMAD4, CDKN1A, TGFB1
 Reactome 3 / 7 161× 5.97e-7 3.12e-5 ✓ sig.
Melanoma
CDH1, CCND1, CDKN1A, EGFR, HRAS
 KEGG 5 / 73 25.7× 1.28e-6 6.06e-5 ✓ sig.
Glioma
CCND1, CDKN1A, EGFR, HRAS, TGFA
 KEGG 5 / 76 24.7× 1.57e-6 7.16e-5 ✓ sig.
Chronic myeloid leukemia
SMAD4, CCND1, CDKN1A, HRAS, TGFB1
 KEGG 5 / 77 24.4× 1.67e-6 7.56e-5 ✓ 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 ⇵
epidermis development
KRT14, CDKN1A, EGFR, SPRR1A, ALDH3A2, KRT5
 GO:0008544 6 / 114 30.7× 3.59e-8 5.12e-6 ✓ sig.
positive regulation of epithelial cell proliferation
ERBB2, EGFR, HRAS, TGFA, TGFB1
 GO:0050679 5 / 73 40.0× 1.47e-7 1.67e-5 ✓ sig.
ERBB2-EGFR signaling pathway
ERBB2, EGFR, TGFA
 GO:0038134 3 / 8 219× 2.54e-7 2.65e-5 ✓ sig.
regulation of cell population proliferation
ERBB2, PTGS2, SMAD4, EGFR, HRAS, TGFB1
 GO:0042127 6 / 201 17.4× 1.03e-6 8.51e-5 ✓ sig.
negative regulation of apoptotic process
BAG1, ERBB2, PTGS2, SOD2, EGFR, TERT, CRYAB, HSPB1
 GO:0043066 8 / 524 8.9× 2.11e-6 1.50e-4 ✓ sig.
positive regulation of fibroblast proliferation
CDKN1A, EGFR, HRAS, TGFB1
 GO:0048146 4 / 55 42.5× 2.27e-6 1.59e-4 ✓ sig.
positive regulation of miRNA transcription
SMAD4, EGFR, TGFB1, TERT
 GO:1902895 4 / 56 41.7× 2.44e-6 1.69e-4 ✓ sig.
cellular response to hypoxia
ATF4, PTGS2, TGFB1, TERT, AQP3
 GO:0071456 5 / 139 21.0× 3.63e-6 2.32e-4 ✓ sig.
cell population proliferation
ERBB2, SMAD4, CCND1, EGFR, ODC1, TGFB1
 GO:0008283 6 / 263 13.3× 4.89e-6 2.95e-4 ✓ sig.
cellular response to growth factor stimulus
ERBB2, SMAD4, EGFR, TGFB1
 GO:0071363 4 / 76 30.7× 8.33e-6 4.53e-4 ✓ sig.
cellular response to gamma radiation
CDKN1A, HRAS, CRYAB
 GO:0071480 3 / 28 62.6× 1.45e-5 6.99e-4 ✓ sig.
response to UV-A
CCND1, EGFR
 GO:0070141 2 / 4 292× 1.70e-5 7.91e-4 ✓ sig.
positive regulation of vascular endothelial growth factor production
ATF4, PTGS2, TGFB1
 GO:0010575 3 / 32 54.7× 2.19e-5 9.63e-4 ✓ sig.
positive regulation of cell population proliferation
CCND1, CDKN1A, EGFR, HRAS, ODC1, TGFA, TGFB1
 GO:0008284 7 / 532 7.7× 2.64e-5 1.11e-3 ✓ sig.
cell surface receptor signaling pathway
BAG1, CD274, ERBB2, EGFR, HRAS, TGFA
 GO:0007166 6 / 373 9.4× 3.55e-5 1.39e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Papilloma Tongue neoplasms 0.150 3 4.33e-8 3.41e-7 ✓ sig.
Ductal carcinoma of breast Papilloma 0.136 3 7.92e-8 5.96e-7 ✓ sig.
Ductal carcinoma of breast Tongue neoplasms 0.095 2 2.50e-5 1.23e-4 ✓ sig.
Dermatopathia pigmentosa reticularis Epidermolysis bullosa simplex 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dermatopathia pigmentosa reticularis Sjogren-larsson syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Epidermolysis bullosa simplex Sjogren-larsson syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dermatopathia pigmentosa reticularis Weber-cockayne syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Epidermolysis bullosa simplex Weber-cockayne syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Sjogren-larsson syndrome Weber-cockayne syndrome 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Dermatopathia pigmentosa reticularis Tongue neoplasms 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Epidermolysis bullosa simplex Tongue neoplasms 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Sjogren-larsson syndrome Tongue neoplasms 0.083 1 1.30e-3 2.04e-3 ✓ sig.