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 206

9 diseases · 26 shared-gene connections
9 Diseases
25 Unique genes
0.333 Avg. similarity score
Appendix neuroendocrine tumor g1 Most-connected disease (7 links)
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Disease Searched: Rectal traditional serrated adenoma 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 ⇵
Appendix neuroendocrine tumor g1 7 7 4
Desmoid tumor 7 7 3
Desmoplastic fibroma 7 7 2
Ovarian microcystic stromal tumor 7 7 3
Rectal traditional serrated adenoma 7 7 7
Angiofibroma 6 6 5
Intestinal neoplasms 5 5 12
Ovarian mixed epithelial tumor 5 5 6
Oligodontia-cancer predisposition syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APC 8 / 9 Angiofibroma, Appendix neuroendocrine tumor g1, Desmoid tumor, Desmoplastic fibroma and 4 more
CTNNB1 8 / 9 Angiofibroma, Appendix neuroendocrine tumor g1, Desmoid tumor, Desmoplastic fibroma and 4 more
TP53 3 / 9 Appendix neuroendocrine tumor g1, Ovarian mixed epithelial tumor, Rectal traditional serrated adenoma
AXIN2 2 / 9 Angiofibroma, Oligodontia-cancer predisposition syndrome
KRAS 2 / 9 Ovarian microcystic stromal tumor, Rectal traditional serrated adenoma
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 ⇵
Endometrial cancer
APC, CTNNB1, BAX, CDKN1A, AXIN2, PTEN, TP53, PIK3CA, KRAS, BRAF
 KEGG 10 / 59 81.4× 1.13e-17 5.80e-15 ✓ sig.
Gastric cancer
APC, CTNNB1, BAX, BCL2, CDKN1A, CDKN1B, MUC2, AXIN2, TP53, PIK3CA, KRAS, BRAF
 KEGG 12 / 150 38.4× 4.17e-17 1.89e-14 ✓ sig.
Hepatocellular carcinoma
APC, CTNNB1, BAX, CDKN1A, PRKCA, AXIN2, PTEN, TP53, PIK3CA, KRAS, BRAF, ARID1A
 KEGG 12 / 170 33.9× 1.94e-16 7.66e-14 ✓ sig.
Colorectal cancer
APC, CTNNB1, BAX, BCL2, CDKN1A, AXIN2, TP53, PIK3CA, KRAS, BRAF
 KEGG 10 / 87 55.2× 6.99e-16 2.49e-13 ✓ sig.
Human papillomavirus infection
APC, CTNNB1, TNF, BAX, CDKN1A, CDKN1B, AXIN2, PTEN, TSC2, TP53, GNAS, PIK3CA
 KEGG 13 / 333 18.8× 1.75e-14 4.75e-12 ✓ sig.
Breast cancer
APC, CTNNB1, BAX, CDKN1A, AXIN2, PTEN, TP53, PIK3CA, KRAS, BRAF
 KEGG 10 / 148 32.5× 1.66e-13 3.67e-11 ✓ sig.
Prostate cancer
CTNNB1, BCL2, CDKN1A, CDKN1B, PTEN, TP53, PIK3CA, KRAS, BRAF
 KEGG 9 / 98 44.1× 2.02e-13 4.42e-11 ✓ sig.
Endocrine resistance
BAX, BCL2, CDKN1A, CDKN1B, TP53, GNAS, PIK3CA, KRAS, BRAF
 KEGG 9 / 99 43.7× 2.22e-13 4.81e-11 ✓ sig.
Pathways in cancer
APC, CTNNB1, BAX, BCL2, CDKN1A, CDKN1B, PRKCA, AXIN2, PTEN, TP53, GNAS, PIK3CA
 KEGG 14 / 533 12.6× 2.76e-13 5.82e-11 ✓ sig.
Glioma
BAX, CDKN1A, PRKCA, PTEN, TP53, PIK3CA, KRAS, BRAF
 KEGG 8 / 76 50.6× 1.75e-12 3.14e-10 ✓ sig.
Human cytomegalovirus infection
CTNNB1, TNF, BAX, CDKN1A, PRKCA, TSC2, TP53, GNAS, PIK3CA, KRAS
 KEGG 10 / 226 21.3× 1.17e-11 1.74e-9 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
TNF, BAX, BCL2, CDKN1B, PRKCA, PRKCD, PIK3CA, KRAS
 KEGG 8 / 101 38.1× 1.81e-11 2.59e-9 ✓ sig.
Hepatitis B
TNF, BAX, BCL2, CDKN1A, PRKCA, TP53, PIK3CA, KRAS, BRAF
 KEGG 9 / 163 26.5× 2.12e-11 2.98e-9 ✓ sig.
Sphingolipid signaling pathway
TNF, BAX, BCL2, PRKCA, PTEN, TP53, PIK3CA, KRAS
 KEGG 8 / 122 31.5× 8.42e-11 1.01e-8 ✓ sig.
Thyroid cancer
CTNNB1, BAX, CDKN1A, TP53, KRAS, BRAF
 KEGG 6 / 37 77.9× 9.48e-11 1.12e-8 ✓ 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 ⇵
negative regulation of cell population proliferation
APC, CTNNB1, TNF, BAX, BCL2, CDKN1A, CDKN1B, AXIN2, PTEN, TSC2, TP53, MEN1
 GO:0008285 12 / 444 20.2× 1.10e-13 6.28e-11 ✓ sig.
regulation of cell cycle
BAX, BCL2, CDKN1A, CDKN1B, PTEN, TSC2, TP53
 GO:0051726 7 / 262 20.0× 3.81e-8 5.60e-6 ✓ sig.
response to gamma radiation
BAX, BCL2, TP53, MEN1
 GO:0010332 4 / 27 111× 4.28e-8 6.22e-6 ✓ sig.
negative regulation of mitotic cell cycle
TNF, BCL2, CDKN1B, TP53
 GO:0045930 4 / 28 107× 4.99e-8 7.06e-6 ✓ sig.
heart development
CTNNB1, CDKN1A, CDKN1B, KCNQ1, PTEN, TSC2, TP53
 GO:0007507 7 / 273 19.2× 5.05e-8 7.14e-6 ✓ sig.
negative regulation of neuron apoptotic process
CTNNB1, BAX, BCL2, PIK3CA, KRAS, BRAF
 GO:0043524 6 / 160 28.0× 5.55e-8 7.73e-6 ✓ sig.
apoptotic signaling pathway
CTNNB1, TNF, BAX, PRKCA, TP53
 GO:0097190 5 / 84 44.5× 8.05e-8 1.06e-5 ✓ sig.
negative regulation of apoptotic signaling pathway
CTNNB1, TNF, BAX, BCL2
 GO:2001234 4 / 36 83.1× 1.43e-7 1.72e-5 ✓ sig.
response to salt stress
TNF, BAX, TP53
 GO:0009651 3 / 9 249× 1.77e-7 2.04e-5 ✓ sig.
negative regulation of cyclin-dependent protein serine/threonine kinase activity
APC, CDKN1B, MEN1
 GO:0045736 3 / 9 249× 1.77e-7 2.04e-5 ✓ sig.
T cell differentiation in thymus
CTNNB1, BCL2, TP53, BRAF
 GO:0033077 4 / 41 72.9× 2.44e-7 2.67e-5 ✓ sig.
DNA damage response
APC, BAX, BCL2, CDKN1A, PRKCD, XPA, TP53, MEN1
 GO:0006974 8 / 577 10.4× 5.35e-7 5.16e-5 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage
TNF, BAX, BCL2, XPA
 GO:0008630 4 / 54 55.4× 7.53e-7 6.80e-5 ✓ sig.
response to UV
CDKN1A, XPA, TP53, MEN1
 GO:0009411 4 / 54 55.4× 7.53e-7 6.80e-5 ✓ sig.
stem cell proliferation
CTNNB1, AXIN2, TP53, RNF43
 GO:0072089 4 / 54 55.4× 7.53e-7 6.80e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Desmoplastic fibroma Ovarian microcystic stromal tumor 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Appendix neuroendocrine tumor g1 Ovarian microcystic stromal tumor 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Appendix neuroendocrine tumor g1 Desmoplastic fibroma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Desmoid tumor Ovarian microcystic stromal tumor 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Desmoid tumor Desmoplastic fibroma 0.500 2 2.50e-8 1.87e-7 ✓ sig.
Ovarian microcystic stromal tumor Ovarian mixed epithelial tumor 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Ovarian microcystic stromal tumor Rectal traditional serrated adenoma 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Desmoplastic fibroma Ovarian mixed epithelial tumor 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Desmoplastic fibroma Rectal traditional serrated adenoma 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Appendix neuroendocrine tumor g1 Desmoid tumor 0.400 2 7.50e-8 5.34e-7 ✓ sig.
Angiofibroma Desmoplastic fibroma 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Angiofibroma Ovarian microcystic stromal tumor 0.333 2 8.34e-8 5.85e-7 ✓ sig.
Desmoid tumor Ovarian mixed epithelial tumor 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Desmoid tumor Rectal traditional serrated adenoma 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Appendix neuroendocrine tumor g1 Ovarian mixed epithelial tumor 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Appendix neuroendocrine tumor g1 Rectal traditional serrated adenoma 0.333 2 1.50e-7 1.02e-6 ✓ sig.
Angiofibroma Appendix neuroendocrine tumor g1 0.286 2 2.50e-7 1.65e-6 ✓ sig.
Angiofibroma Desmoid tumor 0.286 2 2.50e-7 1.65e-6 ✓ sig.
Ovarian mixed epithelial tumor Rectal traditional serrated adenoma 0.286 2 3.00e-7 1.96e-6 ✓ sig.
Angiofibroma Rectal traditional serrated adenoma 0.250 2 5.00e-7 3.18e-6 ✓ sig.
Intestinal neoplasms Ovarian microcystic stromal tumor 0.154 2 5.50e-7 3.46e-6 ✓ sig.
Desmoplastic fibroma Intestinal neoplasms 0.154 2 5.50e-7 3.46e-6 ✓ sig.
Desmoid tumor Intestinal neoplasms 0.143 2 1.65e-6 9.79e-6 ✓ sig.
Appendix neuroendocrine tumor g1 Intestinal neoplasms 0.143 2 1.65e-6 9.79e-6 ✓ sig.
Intestinal neoplasms Rectal traditional serrated adenoma 0.133 2 3.30e-6 1.88e-5 ✓ sig.
Angiofibroma Oligodontia-cancer predisposition syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.