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 30

18 diseases · 34 shared-gene connections
18 Diseases
79 Unique genes
0.217 Avg. similarity score
Brain tumor-polyposis syndrome Most-connected disease (9 links)
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Disease Searched: Bone dysplasia with increased bone density 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 ⇵
Brain tumor-polyposis syndrome 9 9 1
Familial adenomatous polyposis 8 8 1
gastric adenocarcinoma and proximal polyposis of the stomach 8 8 1
Gastrointestinal neoplasms 7 7 4
Cenani-lenz syndrome 6 6 2
Desmoid tumor 5 5 3
Gastrointestinal hemorrhage 3 3 6
Intestinal neoplasms 3 3 12
Intestinal polyps 3 3 6
Macrocytic anemia 3 3 4
Medulloblastoma 3 3 49
Sclerosteosis 3 3 2
congenital myasthenic syndrome 17 2 2 1
Bone dysplasia with increased bone density 1 1 1
Hyperemesis gravidarum 1 1 4
immunodeficiency 97 with autoinflammation 1 1 1
intellectual developmental disorder, autosomal dominant 65 1 1 1
xeroderma pigmentosum group A 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APC 11 / 18 Brain tumor-polyposis syndrome, Cenani-lenz syndrome, Desmoid tumor, Familial adenomatous polyposis and 7 more
CTNNB1 3 / 18 Desmoid tumor, Intestinal neoplasms, Medulloblastoma
LRP4 3 / 18 Cenani-lenz syndrome, congenital myasthenic syndrome 17, Sclerosteosis
ERBB2 2 / 18 Gastrointestinal neoplasms, Medulloblastoma
GDF15 2 / 18 Gastrointestinal neoplasms, Hyperemesis gravidarum
HIC1 2 / 18 Gastrointestinal neoplasms, Medulloblastoma
KDM4B 2 / 18 intellectual developmental disorder, autosomal dominant 65, Medulloblastoma
PIK3CG 2 / 18 immunodeficiency 97 with autoinflammation, Medulloblastoma
SOST 2 / 18 Bone dysplasia with increased bone density, Sclerosteosis
XPA 2 / 18 Intestinal neoplasms, xeroderma pigmentosum group A
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 ⇵
Pathways in cancer
APC, TERT, CTNNB1, SUFU, ERBB2, BAX, BCL2, CDKN1A, CDKN1B, PRKCA, CCND1, JUN
 KEGG 25 / 533 7.1× 2.31e-15 7.58e-13 ✓ sig.
MicroRNAs in cancer
APC, ERBB2, BCL2, CDKN1A, CDKN1B, PRKCA, CCND1, PTGS2, CCNE1, CDK6, DNMT1, IRS2
 KEGG 16 / 311 7.8× 1.38e-10 1.83e-8 ✓ sig.
Gastric cancer
APC, TERT, CTNNB1, ERBB2, BAX, BCL2, CDKN1A, CDKN1B, MUC2, CCND1, CCNE1, MYC
 KEGG 12 / 150 12.2× 2.31e-10 2.88e-8 ✓ sig.
Small cell lung cancer
BAX, BCL2, CDKN1A, CDKN1B, CCND1, PTGS2, CCNE1, CDK6, MYC, SKP2
 KEGG 10 / 93 16.3× 4.39e-10 5.11e-8 ✓ sig.
Breast cancer
APC, CTNNB1, ERBB2, BAX, CDKN1A, CCND1, JUN, BRCA2, CDK6, ESR2, MYC
 KEGG 11 / 148 11.3× 3.02e-9 2.91e-7 ✓ sig.
Basal cell carcinoma
APC, CTNNB1, SUFU, BAX, CDKN1A, PTCH1, PTCH2, SMO
 KEGG 8 / 63 19.3× 7.06e-9 6.21e-7 ✓ sig.
Epstein-Barr virus infection
TNF, BAX, BCL2, CDKN1A, CDKN1B, CCND1, JUN, CCNE1, CDK6, MYC, SKP2, STAT3
 KEGG 12 / 204 8.9× 7.88e-9 6.87e-7 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
TNF, BAX, BCL2, CDKN1B, PRKCA, PRKCD, CCND1, JUN, STAT3
 KEGG 9 / 101 13.5× 1.85e-8 1.46e-6 ✓ sig.
Non-small cell lung cancer
ERBB2, BAX, CDKN1A, PRKCA, CCND1, CDK6, RASSF1, STAT3
 KEGG 8 / 73 16.7× 2.32e-8 1.80e-6 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
TNF, BCL6, IRF4, BCL2, CDKN1A, CCND1, PTGS2, MYC, STAT3
 Reactome 9 / 108 12.7× 3.35e-8 2.48e-6 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
CTNNB1, CSF2, BAX, CDKN1A, CCND1, JUN, PTGS2, CDK6, MYC, PIK3CG, STAT3
 KEGG 11 / 196 8.5× 5.67e-8 3.97e-6 ✓ sig.
Hedgehog signaling pathway
SUFU, BCL2, CCND1, GPR161, PTCH1, PTCH2, SMO
 KEGG 7 / 56 19.0× 7.28e-8 4.96e-6 ✓ sig.
Proteoglycans in cancer
CTNNB1, TNF, ERBB2, CDKN1A, PRKCA, CCND1, MYC, PTCH1, SMO, STAT3, VAV1
 KEGG 11 / 204 8.2× 8.54e-8 5.72e-6 ✓ sig.
Colorectal cancer
APC, CTNNB1, BAX, BCL2, CDKN1A, CCND1, JUN, MYC
 KEGG 8 / 87 14.0× 9.38e-8 6.21e-6 ✓ sig.
Hepatitis B
TNF, BAX, BCL2, CDKN1A, PRKCA, JUN, CCNE1, DDX3X, MYC, STAT3
 KEGG 10 / 163 9.3× 1.04e-7 6.75e-6 ✓ 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 ⇵
cell population proliferation
CTNNB1, BCL6, CSF2, ERBB2, BAX, BCL2, CCND1, JUN, BRCA2, CDK9, IRS2, MYC
 GO:0008283 15 / 263 13.5× 2.73e-13 1.37e-10 ✓ sig.
regulation of cell population proliferation
CTNNB1, TNF, BCL6, CSF2, ERBB2, JUN, PTGS1, PTGS2, CDK6, DNMT1, PTCH1, STAT3
 GO:0042127 12 / 201 14.1× 4.70e-11 1.45e-8 ✓ sig.
negative regulation of apoptotic process
TERT, CTNNB1, TNF, AVP, BCL6, LTF, ERBB2, BCL2, NR1H4, PRKCD, GNRH1, JUN
 GO:0043066 17 / 524 7.7× 5.08e-11 1.55e-8 ✓ sig.
regulation of cell cycle
BAX, BCL2, CDKN1A, CDKN1B, CCND1, JUN, CCNE1, CDK6, CDK9, RASSF1, SKP2, STAT3
 GO:0051726 12 / 262 10.8× 9.99e-10 2.17e-7 ✓ sig.
G1/S transition of mitotic cell cycle
BCL2, CDKN1A, CDKN1B, CCND1, CCNE1, CDK6, MYC, SKP2
 GO:0000082 8 / 85 22.3× 2.63e-9 5.13e-7 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage
TNF, HIC1, BAX, BCL2, XPA, BRCA2, MYC
 GO:0008630 7 / 54 30.7× 2.78e-9 5.38e-7 ✓ sig.
negative regulation of DNA-templated transcription
CTNNB1, TNF, BCL6, CSF2, CDKN1B, JUN, DNMT1, EHMT1, KAT6A, L3MBTL2, L3MBTL3, PRAME
 GO:0045892 16 / 631 6.0× 7.07e-9 1.23e-6 ✓ sig.
positive regulation of DNA-templated transcription
CTNNB1, TNF, IRF4, NR1H4, JUN, BRCA2, BRD4, ESR2, FLI1, KAT6A, MYC, MYCN
 GO:0045893 17 / 778 5.2× 2.02e-8 3.12e-6 ✓ sig.
positive regulation of cell population proliferation
CTNNB1, AVP, CSF2, BCL2, CDKN1A, CDKN1B, CCND1, IRS2, KDM4C, MYC, PDGFRA, PRAME
 GO:0008284 14 / 532 6.2× 4.41e-8 6.10e-6 ✓ sig.
positive regulation of mesenchymal cell proliferation
CTNNB1, IRS2, MYC, MYCN, SMO
 GO:0002053 5 / 26 45.5× 7.29e-8 9.33e-6 ✓ sig.
positive regulation of fibroblast proliferation
CDKN1A, JUN, CDK6, MYC, PDGFRA, S100A6
 GO:0048146 6 / 55 25.8× 1.16e-7 1.38e-5 ✓ sig.
regulation of gene expression
CTNNB1, CSF2, BCL2, GNRH1, BRD2, CDK6, DNMT1, KDM4B, KDM4C, MYC, PRMT5, SMO
 GO:0010468 12 / 402 7.1× 1.16e-7 1.39e-5 ✓ sig.
DNA damage response
APC, BCL6, BAX, BCL2, CDKN1A, PRKCD, XPA, CCND1, BRCA2, BRD4, CDK6, CDK9
 GO:0006974 14 / 577 5.7× 1.20e-7 1.43e-5 ✓ sig.
positive regulation of miRNA transcription
TERT, TNF, JUN, MYC, MYCN, STAT3
 GO:1902895 6 / 56 25.3× 1.29e-7 1.52e-5 ✓ sig.
positive regulation of gene expression
CTNNB1, TNF, AVP, CSF2, ERBB2, CDK6, DDX3X, DNMT1, KAT6A, MYC, MYCN, SMO
 GO:0010628 13 / 504 6.1× 1.78e-7 1.99e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Gastrointestinal neoplasms Medulloblastoma 0.059 3 1.21e-7 8.42e-7 ✓ sig.
Desmoid tumor Intestinal neoplasms 0.143 2 1.67e-6 9.46e-6 ✓ sig.
Brain tumor-polyposis syndrome Familial adenomatous polyposis 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Familial adenomatous polyposis gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Brain tumor-polyposis syndrome gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Cenani-lenz syndrome Familial adenomatous polyposis 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Cenani-lenz syndrome gastric adenocarcinoma and proximal polyposis of the stomach 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Cenani-lenz syndrome congenital myasthenic syndrome 17 0.333 1 1.30e-4 3.91e-4 ✓ sig.
congenital myasthenic syndrome 17 Sclerosteosis 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Brain tumor-polyposis syndrome Cenani-lenz syndrome 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Bone dysplasia with increased bone density Sclerosteosis 0.333 1 1.30e-4 3.91e-4 ✓ sig.
Brain tumor-polyposis syndrome Desmoid tumor 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Desmoid tumor Familial adenomatous polyposis 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Desmoid tumor gastric adenocarcinoma and proximal polyposis of the stomach 0.250 1 1.95e-4 5.32e-4 ✓ sig.
Cenani-lenz syndrome Sclerosteosis 0.250 1 2.60e-4 6.48e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Macrocytic anemia 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Familial adenomatous polyposis Macrocytic anemia 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Brain tumor-polyposis syndrome Macrocytic anemia 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Familial adenomatous polyposis Gastrointestinal neoplasms 0.200 1 2.60e-4 6.48e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Gastrointestinal neoplasms 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastrointestinal neoplasms 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Brain tumor-polyposis syndrome Intestinal polyps 0.143 1 3.90e-4 8.64e-4 ✓ sig.
Familial adenomatous polyposis Intestinal polyps 0.143 1 3.90e-4 8.64e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Intestinal polyps 0.143 1 3.90e-4 8.64e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Gastrointestinal hemorrhage 0.143 1 3.90e-4 8.64e-4 ✓ sig.
Familial adenomatous polyposis Gastrointestinal hemorrhage 0.143 1 3.90e-4 8.64e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastrointestinal hemorrhage 0.143 1 3.90e-4 8.64e-4 ✓ sig.
Cenani-lenz syndrome Gastrointestinal neoplasms 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Desmoid tumor Gastrointestinal neoplasms 0.143 1 7.79e-4 1.40e-3 ✓ sig.
Brain tumor-polyposis syndrome Intestinal neoplasms 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Intestinal neoplasms xeroderma pigmentosum group A 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Gastrointestinal neoplasms Hyperemesis gravidarum 0.125 1 1.04e-3 1.74e-3 ✓ sig.
immunodeficiency 97 with autoinflammation Medulloblastoma 0.020 1 3.18e-3 4.17e-3 ✓ sig.
intellectual developmental disorder, autosomal dominant 65 Medulloblastoma 0.020 1 3.18e-3 4.17e-3 ✓ sig.