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 88

12 diseases · 26 shared-gene connections
12 Diseases
32 Unique genes
0.226 Avg. similarity score
Adrenocortical carcinoma Most-connected disease (9 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 ⇵
Adrenocortical carcinoma 9 9 1
Choroid plexus carcinoma 9 9 1
Choroid plexus papilloma 8 8 1
Urologic neoplasms 5 5 8
B-cell chronic lymphocytic leukemia 4 4 8
Central nervous system neoplasms 3 3 2
Chromosome 17 deletion 3 3 2
Sapho syndrome 3 3 5
Small cell carcinoma 3 3 9
Urogenital neoplasms 3 3 5
Familial telangiectasia cancer syndrome 1 1 1
Uinary system neoplasms 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
TP53 10 / 12 Adrenocortical carcinoma, B-cell chronic lymphocytic leukemia, Central nervous system neoplasms, Choroid plexus carcinoma and 6 more
ATR 2 / 12 Familial telangiectasia cancer syndrome, Urologic neoplasms
CCND1 2 / 12 B-cell chronic lymphocytic leukemia, Urologic neoplasms
SLC2A13 2 / 12 Uinary system neoplasms, Urogenital neoplasms
WDR11 2 / 12 Uinary system neoplasms, Urogenital 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 ⇵
Bladder cancer
TP53, CCND1, RB1, MDM2, CDKN2A, VEGFA
 KEGG 6 / 41 54.9× 9.17e-10 1.04e-7 ✓ sig.
Cellular senescence
TP53, ATM, CCND1, MTOR, RB1, ATR, MDM2, CDKN2A
 KEGG 8 / 157 19.1× 5.75e-9 5.40e-7 ✓ sig.
Human papillomavirus infection
TP53, ATM, CCND1, MTOR, RB1, ATR, MDM2, TNF, WNT7A, VEGFA
 KEGG 10 / 333 11.3× 8.80e-9 7.83e-7 ✓ sig.
Stabilization of p53
TP53, ATM, MDM2, CDKN2A
 Reactome 4 / 11 136× 1.35e-8 1.13e-6 ✓ sig.
Regulation of TP53 Degradation
TP53, ATM, MTOR, MDM2, CDKN2A
 Reactome 5 / 36 52.1× 3.44e-8 2.57e-6 ✓ sig.
p53 signaling pathway
TP53, ATM, CCND1, ATR, MDM2, CDKN2A
 KEGG 6 / 75 30.0× 3.86e-8 2.83e-6 ✓ sig.
Glioma
TP53, CCND1, MTOR, RB1, MDM2, CDKN2A
 KEGG 6 / 76 29.6× 4.18e-8 3.03e-6 ✓ sig.
Pancreatic cancer
TP53, CCND1, MTOR, RB1, CDKN2A, VEGFA
 KEGG 6 / 77 29.2× 4.52e-8 3.26e-6 ✓ sig.
Human cytomegalovirus infection
TP53, CCND1, MTOR, RB1, MDM2, TNF, CDKN2A, VEGFA
 KEGG 8 / 226 13.3× 9.90e-8 6.47e-6 ✓ sig.
Cell cycle
TP53, ATM, CCND1, RB1, ATR, MDM2, CDKN2A
 KEGG 7 / 158 16.6× 1.52e-7 9.44e-6 ✓ sig.
Endocrine resistance
TP53, CCND1, MTOR, RB1, MDM2, CDKN2A
 KEGG 6 / 99 22.7× 2.05e-7 1.22e-5 ✓ sig.
Hepatocellular carcinoma
TP53, CCND1, MTOR, RB1, SMARCA4, CDKN2A, WNT7A
 KEGG 7 / 170 15.5× 2.51e-7 1.46e-5 ✓ sig.
Proteoglycans in cancer
TP53, CCND1, MTOR, MDM2, TNF, WNT7A, VEGFA
 KEGG 7 / 204 12.9× 8.64e-7 4.30e-5 ✓ sig.
Melanoma
TP53, CCND1, RB1, MDM2, CDKN2A
 KEGG 5 / 73 25.7× 1.28e-6 6.06e-5 ✓ sig.
Non-small cell lung cancer
TP53, CCND1, RB1, CDKN2A, FHIT
 KEGG 5 / 73 25.7× 1.28e-6 6.06e-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 ⇵
replicative senescence
TP53, ATM, ATR, CDKN2A
 GO:0090399 4 / 16 146× 1.27e-8 2.10e-6 ✓ sig.
cellular response to gamma radiation
TP53, ATM, ATR, MDM2
 GO:0071480 4 / 28 83.4× 1.41e-7 1.62e-5 ✓ sig.
intrinsic apoptotic signaling pathway by p53 class mediator
TP53, PYCARD, FHIT, WWOX
 GO:0072332 4 / 29 80.5× 1.63e-7 1.83e-5 ✓ sig.
regulation of cell cycle
TP53, ATM, CCND1, RB1, BAP1, MDM2, CDKN2A
 GO:0051726 7 / 262 15.6× 2.45e-7 2.58e-5 ✓ sig.
apoptotic process
TP53, BIRC5, PYCARD, RB1, MDM2, CDKN2A, WNT7A, FHIT, VEGFA, WWOX
 GO:0006915 10 / 747 7.8× 2.85e-7 2.92e-5 ✓ sig.
apoptotic signaling pathway
TP53, P2RX7, PYCARD, TNF, CDKN2A
 GO:0097190 5 / 84 34.8× 2.98e-7 3.03e-5 ✓ sig.
positive regulation of signal transduction by p53 class mediator
RPS15, SMARCA4, CDKN2A
 GO:1901798 3 / 13 135× 1.29e-6 1.01e-4 ✓ sig.
negative regulation of cell growth
TP53, NPPA, RB1, SMARCA4, CDKN2A
 GO:0030308 5 / 115 25.4× 1.43e-6 1.10e-4 ✓ sig.
positive regulation of gene expression
TP53, ATM, P2RX7, MDM2, TNF, CDKN2A, WNT7A, VEGFA
 GO:0010628 8 / 504 9.3× 1.57e-6 1.19e-4 ✓ sig.
regulation of cellular response to heat
ATM, MTOR, ATR
 GO:1900034 3 / 15 117× 2.05e-6 1.47e-4 ✓ sig.
regulation of G1/S transition of mitotic cell cycle
CCND1, RB1, SMARCA4, CDKN2A
 GO:2000045 4 / 57 41.0× 2.62e-6 1.79e-4 ✓ sig.
establishment of RNA localization to telomere
ATM, ATR
 GO:0097694 2 / 2 584× 2.84e-6 1.90e-4 ✓ sig.
establishment of protein-containing complex localization to telomere
ATM, ATR
 GO:0097695 2 / 2 584× 2.84e-6 1.90e-4 ✓ sig.
positive regulation of telomerase catalytic core complex assembly
ATM, ATR
 GO:1904884 2 / 2 584× 2.84e-6 1.90e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
TP53, ATM, IKZF3, RB1, SMARCA4, TNF, CDKN2A, WNT7A, OGG1, VEGFA, WWOX
 GO:0045944 11 / 1,208 5.3× 2.87e-6 1.92e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Uinary system neoplasms Urogenital neoplasms 0.333 2 8.44e-8 6.27e-7 ✓ sig.
B-cell chronic lymphocytic leukemia Urologic neoplasms 0.133 2 6.60e-6 3.54e-5 ✓ sig.
Adrenocortical carcinoma Choroid plexus papilloma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Choroid plexus carcinoma Choroid plexus papilloma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Adrenocortical carcinoma Choroid plexus carcinoma 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Adrenocortical carcinoma Chromosome 17 deletion 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Central nervous system neoplasms Choroid plexus carcinoma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Central nervous system neoplasms Choroid plexus papilloma 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Adrenocortical carcinoma Central nervous system neoplasms 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Choroid plexus carcinoma Chromosome 17 deletion 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Choroid plexus papilloma Chromosome 17 deletion 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Choroid plexus carcinoma Urogenital neoplasms 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Adrenocortical carcinoma Sapho syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Choroid plexus carcinoma Sapho syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Choroid plexus papilloma Sapho syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Adrenocortical carcinoma Urogenital neoplasms 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Choroid plexus carcinoma Urologic neoplasms 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Adrenocortical carcinoma Urologic neoplasms 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Choroid plexus papilloma Urologic neoplasms 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Familial telangiectasia cancer syndrome Urologic neoplasms 0.111 1 5.20e-4 1.04e-3 ✓ sig.
B-cell chronic lymphocytic leukemia Choroid plexus papilloma 0.111 1 5.20e-4 1.04e-3 ✓ sig.
B-cell chronic lymphocytic leukemia Choroid plexus carcinoma 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Adrenocortical carcinoma B-cell chronic lymphocytic leukemia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Choroid plexus papilloma Small cell carcinoma 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Choroid plexus carcinoma Small cell carcinoma 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Adrenocortical carcinoma Small cell carcinoma 0.100 1 5.84e-4 1.14e-3 ✓ sig.