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 70

13 diseases · 27 shared-gene connections
13 Diseases
68 Unique genes
0.216 Avg. similarity score
Brain tumor-polyposis syndrome Most-connected disease (8 links)
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Disease Searched: Gastrointestinal hemorrhage 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 8 8 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 4 4 2
Desmoid tumor 4 4 3
Gastrointestinal hemorrhage 3 3 6
Intestinal polyps 3 3 6
Macrocytic anemia 3 3 4
Medulloblastoma 3 3 49
Hyperemesis gravidarum 1 1 4
immunodeficiency 97 with autoinflammation 1 1 1
intellectual developmental disorder, autosomal dominant 65 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
APC 10 / 13 Brain tumor-polyposis syndrome, Cenani-lenz syndrome, Desmoid tumor, Familial adenomatous polyposis and 6 more
CTNNB1 2 / 13 Desmoid tumor, Medulloblastoma
ERBB2 2 / 13 Gastrointestinal neoplasms, Medulloblastoma
GDF15 2 / 13 Gastrointestinal neoplasms, Hyperemesis gravidarum
HIC1 2 / 13 Gastrointestinal neoplasms, Medulloblastoma
KDM4B 2 / 13 intellectual developmental disorder, autosomal dominant 65, Medulloblastoma
PIK3CG 2 / 13 immunodeficiency 97 with autoinflammation, Medulloblastoma
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, CCND1, JUN, PTGS2, BRCA2, CCNE1, CDK6, ESR2
 KEGG 20 / 533 6.6× 6.94e-12 1.21e-9 ✓ sig.
Breast cancer
APC, CTNNB1, ERBB2, CCND1, JUN, BRCA2, CDK6, ESR2, MYC
 KEGG 9 / 148 10.7× 1.36e-7 8.30e-6 ✓ sig.
MicroRNAs in cancer
APC, ERBB2, CCND1, PTGS2, CCNE1, CDK6, DNMT1, IRS2, MYC, PDGFRA, RASSF1, STAT3
 KEGG 12 / 311 6.8× 1.46e-7 8.81e-6 ✓ sig.
Hedgehog signaling pathway
SUFU, CCND1, GPR161, PTCH1, PTCH2, SMO
 KEGG 6 / 56 18.9× 6.84e-7 3.35e-5 ✓ sig.
Basal cell carcinoma
APC, CTNNB1, SUFU, PTCH1, PTCH2, SMO
 KEGG 6 / 63 16.8× 1.39e-6 6.24e-5 ✓ sig.
Kaposi sarcoma-associated herpesvirus infection
CTNNB1, CSF2, CCND1, JUN, PTGS2, CDK6, MYC, PIK3CG, STAT3
 KEGG 9 / 196 8.1× 1.47e-6 6.52e-5 ✓ sig.
Proteoglycans in cancer
CTNNB1, TNF, ERBB2, CCND1, MYC, PTCH1, SMO, STAT3, VAV1
 KEGG 9 / 204 7.8× 2.04e-6 8.58e-5 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
TNF, BCL6, IRF4, CCND1, PTGS2, MYC, STAT3
 Reactome 7 / 108 11.4× 2.41e-6 9.97e-5 ✓ sig.
RUNX3 regulates WNT signaling
CTNNB1, CCND1, MYC
 Reactome 3 / 8 66.2× 9.53e-6 3.11e-4 ✓ sig.
Small cell lung cancer
CCND1, PTGS2, CCNE1, CDK6, MYC, SKP2
 KEGG 6 / 93 11.4× 1.36e-5 4.23e-4 ✓ sig.
Epstein-Barr virus infection
TNF, CCND1, JUN, CCNE1, CDK6, MYC, SKP2, STAT3
 KEGG 8 / 204 6.9× 1.86e-5 5.51e-4 ✓ sig.
Endometrial cancer
APC, CTNNB1, ERBB2, CCND1, MYC
 KEGG 5 / 59 15.0× 1.98e-5 5.79e-4 ✓ sig.
Gastric cancer
APC, TERT, CTNNB1, ERBB2, CCND1, CCNE1, MYC
 KEGG 7 / 150 8.2× 2.11e-5 6.12e-4 ✓ sig.
Human cytomegalovirus infection
CTNNB1, TNF, CCND1, PTGS2, CDK6, MYC, PDGFRA, STAT3
 KEGG 8 / 226 6.3× 3.89e-5 1.01e-3 ✓ sig.
Non-small cell lung cancer
ERBB2, CCND1, CDK6, RASSF1, STAT3
 KEGG 5 / 73 12.1× 5.59e-5 1.35e-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 ⇵
regulation of cell population proliferation
CTNNB1, TNF, BCL6, CSF2, ERBB2, JUN, PTGS1, PTGS2, CDK6, DNMT1, PTCH1, STAT3
 GO:0042127 12 / 201 16.4× 7.41e-12 2.80e-9 ✓ sig.
cell population proliferation
CTNNB1, BCL6, CSF2, ERBB2, CCND1, JUN, BRCA2, CDK9, IRS2, MYC, MYCN, SMO
 GO:0008283 13 / 263 13.6× 9.96e-12 3.67e-9 ✓ sig.
negative regulation of apoptotic process
TERT, CTNNB1, TNF, AVP, BCL6, LTF, ERBB2, GNRH1, JUN, PTGS2, DDX3X, MYC
 GO:0043066 14 / 524 7.3× 4.80e-9 8.85e-7 ✓ sig.
negative regulation of DNA-templated transcription
CTNNB1, TNF, BCL6, CSF2, JUN, DNMT1, EHMT1, KAT6A, L3MBTL2, L3MBTL3, PRAME, PRMT5
 GO:0045892 15 / 631 6.5× 6.06e-9 1.09e-6 ✓ sig.
positive regulation of gene expression
CTNNB1, TNF, AVP, CSF2, ERBB2, CDK6, DDX3X, DNMT1, KAT6A, MYC, MYCN, SMO
 GO:0010628 13 / 504 7.1× 2.77e-8 4.05e-6 ✓ sig.
positive regulation of mesenchymal cell proliferation
CTNNB1, IRS2, MYC, MYCN, SMO
 GO:0002053 5 / 26 52.8× 3.41e-8 4.81e-6 ✓ sig.
positive regulation of miRNA transcription
TERT, TNF, JUN, MYC, MYCN, STAT3
 GO:1902895 6 / 56 29.4× 5.22e-8 6.93e-6 ✓ sig.
positive regulation of DNA-templated transcription
CTNNB1, TNF, IRF4, JUN, BRCA2, BRD4, ESR2, FLI1, KAT6A, MYC, MYCN, OTX2
 GO:0045893 15 / 778 5.3× 9.68e-8 1.16e-5 ✓ sig.
regulation of DNA-templated transcription
SUFU, IRF4, HIC1, JUN, BRCA2, BRD2, BRD3, BRD4, ESR2, FLI1, KAT6A, L3MBTL2
 GO:0006355 20 / 1,454 3.8× 1.27e-7 1.47e-5 ✓ sig.
positive regulation of transcription by RNA polymerase II
CTNNB1, TNF, IRF4, JUN, ATOH1, BRD3, BRD4, CDK9, DDX3X, ESR2, FLI1, KDM4C
 GO:0045944 18 / 1,208 4.1× 1.97e-7 2.13e-5 ✓ sig.
regulation of gene expression
CTNNB1, CSF2, GNRH1, BRD2, CDK6, DNMT1, KDM4B, KDM4C, MYC, PRMT5, SMO
 GO:0010468 11 / 402 7.5× 2.03e-7 2.19e-5 ✓ sig.
negative regulation of transcription by RNA polymerase II
CTNNB1, TNF, SUFU, BCL6, HIC1, CCND1, JUN, CCNE1, CDK6, DNMT1, EHMT1, ESR2
 GO:0000122 16 / 1,002 4.4× 4.37e-7 4.16e-5 ✓ sig.
chromatin organization
BRD2, BRD3, BRD4, DNMT1, EHMT1, KAT6A, KDM4B, KDM4C, L3MBTL2, L3MBTL3, PRMT5
 GO:0006325 11 / 449 6.7× 6.09e-7 5.50e-5 ✓ sig.
positive regulation of fibroblast proliferation
JUN, CDK6, MYC, PDGFRA, S100A6
 GO:0048146 5 / 55 25.0× 1.66e-6 1.25e-4 ✓ sig.
Wnt signaling pathway
APC, LRP4, CTNNB1, HIC1, CCND1, CCNE1, DDX3X, MYC
 GO:0016055 8 / 232 9.5× 1.95e-6 1.42e-4 ✓ 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 8.40e-7 ✓ sig.
Brain tumor-polyposis syndrome gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Familial adenomatous polyposis gastric adenocarcinoma and proximal polyposis of the stomach 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Brain tumor-polyposis syndrome Familial adenomatous polyposis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Cenani-lenz syndrome Familial adenomatous polyposis 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Brain tumor-polyposis syndrome Cenani-lenz syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Cenani-lenz syndrome gastric adenocarcinoma and proximal polyposis of the stomach 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Brain tumor-polyposis syndrome Desmoid tumor 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Desmoid tumor Familial adenomatous polyposis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Desmoid tumor gastric adenocarcinoma and proximal polyposis of the stomach 0.250 1 1.95e-4 5.35e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Macrocytic anemia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastrointestinal neoplasms 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Familial adenomatous polyposis Gastrointestinal neoplasms 0.200 1 2.60e-4 6.51e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Gastrointestinal neoplasms 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Familial adenomatous polyposis Macrocytic anemia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Brain tumor-polyposis syndrome Macrocytic anemia 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Familial adenomatous polyposis Gastrointestinal hemorrhage 0.143 1 3.90e-4 8.66e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Intestinal polyps 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Familial adenomatous polyposis Intestinal polyps 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Brain tumor-polyposis syndrome Intestinal polyps 0.143 1 3.90e-4 8.66e-4 ✓ sig.
gastric adenocarcinoma and proximal polyposis of the stomach Gastrointestinal hemorrhage 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Brain tumor-polyposis syndrome Gastrointestinal hemorrhage 0.143 1 3.90e-4 8.66e-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.
Gastrointestinal neoplasms Hyperemesis gravidarum 0.125 1 1.04e-3 1.74e-3 ✓ sig.
intellectual developmental disorder, autosomal dominant 65 Medulloblastoma 0.020 1 3.18e-3 4.17e-3 ✓ sig.
immunodeficiency 97 with autoinflammation Medulloblastoma 0.020 1 3.18e-3 4.17e-3 ✓ sig.