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 80

13 diseases · 41 shared-gene connections
13 Diseases
22 Unique genes
0.333 Avg. similarity score
11p partial monosomy syndrome Most-connected disease (10 links)
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Disease Searched: Meacham syndrome 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 ⇵
11p partial monosomy syndrome 10 10 1
Denys drash syndrome 10 10 1
Frasier syndrome 10 10 1
Wilms tumor 1 10 10 1
Peritoneal multicystic mesothelioma 8 8 1
Peritoneal neoplasms 7 7 10
Ambiguous genitalia 5 5 5
Anus neoplasms 5 5 9
Meacham syndrome 5 5 1
Nephrogenic rest 5 5 1
Wagner syndrome 5 5 2
Cataract 30, pulverulent 1 1 1
Tubulointerstitial kidney disease, autosomal dominant, 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
WT1 11 / 13 11p partial monosomy syndrome, Ambiguous genitalia, Anus neoplasms, Denys drash syndrome and 7 more
FLNA 2 / 13 Ambiguous genitalia, Anus neoplasms
MUC1 2 / 13 Peritoneal neoplasms, Tubulointerstitial kidney disease, autosomal dominant, 2
VIM 2 / 13 Cataract 30, pulverulent, Peritoneal 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 ⇵
Proteoglycans in cancer
FLNA, CTNNB1, ERBB3, KRAS, TP53
 KEGG 5 / 204 13.4× 2.80e-5 6.85e-4 ✓ sig.
Thyroid cancer
CTNNB1, KRAS, TP53
 KEGG 3 / 37 44.3× 3.98e-5 9.12e-4 ✓ sig.
Transcriptional Regulation by VENTX
CTNNB1, CDKN2A, TP53
 Reactome 3 / 38 43.1× 4.32e-5 9.75e-4 ✓ sig.
Human cytomegalovirus infection
IFNB1, CTNNB1, CDKN2A, KRAS, TP53
 KEGG 5 / 226 12.1× 4.58e-5 1.02e-3 ✓ sig.
Bladder cancer
CDKN2A, KRAS, TP53
 KEGG 3 / 41 39.9× 5.44e-5 1.16e-3 ✓ sig.
Thyroid hormone signaling pathway
CTNNB1, SLC2A1, KRAS, TP53
 KEGG 4 / 122 17.9× 6.44e-5 1.33e-3 ✓ sig.
RUNX3 regulates CDKN1A transcription
ZFHX3, TP53
 Reactome 2 / 7 156× 6.69e-5 1.37e-3 ✓ sig.
Endometrial cancer
CTNNB1, KRAS, TP53
 KEGG 3 / 59 27.8× 1.62e-4 2.78e-3 ✓ sig.
Stabilization of p53
CDKN2A, TP53
 Reactome 2 / 11 99.3× 1.74e-4 2.95e-3 ✓ sig.
Hepatitis C
IFNB1, CTNNB1, KRAS, TP53
 KEGG 4 / 159 13.7× 1.80e-4 3.01e-3 ✓ sig.
MicroRNAs in cancer
VIM, CDKN2A, ERBB3, KRAS, TP53
 KEGG 5 / 311 8.8× 2.07e-4 3.37e-3 ✓ sig.
Hepatocellular carcinoma
CTNNB1, CDKN2A, KRAS, TP53
 KEGG 4 / 170 12.8× 2.32e-4 3.69e-3 ✓ sig.
Central carbon metabolism in cancer
SLC2A1, KRAS, TP53
 KEGG 3 / 71 23.1× 2.81e-4 4.29e-3 ✓ sig.
Melanoma
CDKN2A, KRAS, TP53
 KEGG 3 / 73 22.4× 3.05e-4 4.57e-3 ✓ sig.
Non-small cell lung cancer
CDKN2A, KRAS, TP53
 KEGG 3 / 73 22.4× 3.05e-4 4.57e-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 ⇵
positive regulation of gene expression
WT1, CTNNB1, VIM, CDKN2A, ERBB3, KRAS, TP53
 GO:0010628 7 / 504 11.8× 1.19e-6 9.95e-5 ✓ sig.
negative regulation of apoptotic process
WT1, FLNA, POR, CTNNB1, PDPN, ERBB3, TP53
 GO:0043066 7 / 524 11.3× 1.55e-6 1.23e-4 ✓ sig.
heart development
WT1, FREM2, CTNNB1, ERBB3, TP53
 GO:0007507 5 / 273 15.6× 1.38e-5 6.98e-4 ✓ sig.
cellular response to gonadotropin stimulus
WT1, POR
 GO:0071371 2 / 7 243× 2.77e-5 1.18e-3 ✓ sig.
mesenchymal to epithelial transition
WT1, CTNNB1
 GO:0060231 2 / 11 154× 7.23e-5 2.43e-3 ✓ sig.
myoblast proliferation
CTNNB1, KRAS
 GO:0051450 2 / 12 142× 8.67e-5 2.78e-3 ✓ sig.
cell adhesion
FREM2, CTNNB1, MCAM, PDPN, VCAN, CTNND2
 GO:0007155 6 / 665 7.7× 9.09e-5 2.88e-3 ✓ sig.
Ras protein signal transduction
CDKN2A, KRAS, TP53
 GO:0007265 3 / 79 32.3× 1.06e-4 3.23e-3 ✓ sig.
apoptotic signaling pathway
CTNNB1, CDKN2A, TP53
 GO:0097190 3 / 84 30.3× 1.27e-4 3.67e-3 ✓ sig.
rRNA transcription
CDKN2A, TP53
 GO:0009303 2 / 15 113× 1.38e-4 3.88e-3 ✓ sig.
wound healing, spreading of cells
FLNA, PDPN
 GO:0044319 2 / 15 113× 1.38e-4 3.88e-3 ✓ sig.
negative regulation of cell population proliferation
WT1, CTNNB1, PDPN, CDKN2A, TP53
 GO:0008285 5 / 444 9.6× 1.40e-4 3.92e-3 ✓ sig.
replicative senescence
CDKN2A, TP53
 GO:0090399 2 / 16 106× 1.57e-4 4.29e-3 ✓ sig.
mitotic G1 DNA damage checkpoint signaling
MUC1, TP53
 GO:0031571 2 / 16 106× 1.57e-4 4.29e-3 ✓ sig.
glial cell proliferation
KRAS, TP53
 GO:0014009 2 / 18 94.4× 2.00e-4 5.09e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Ambiguous genitalia Anus neoplasms 0.182 2 1.75e-6 1.03e-5 ✓ sig.
11p partial monosomy syndrome Frasier syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Peritoneal multicystic mesothelioma Wilms tumor 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nephrogenic rest Peritoneal multicystic mesothelioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Nephrogenic rest Wilms tumor 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Meacham syndrome Peritoneal multicystic mesothelioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Meacham syndrome Wilms tumor 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Frasier syndrome Meacham syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Denys drash syndrome Meacham syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
11p partial monosomy syndrome Meacham syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Frasier syndrome Nephrogenic rest 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Frasier syndrome Peritoneal multicystic mesothelioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Frasier syndrome Wilms tumor 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Denys drash syndrome Nephrogenic rest 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Denys drash syndrome Peritoneal multicystic mesothelioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Denys drash syndrome Wilms tumor 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Denys drash syndrome Frasier syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
11p partial monosomy syndrome Denys drash syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
11p partial monosomy syndrome Wilms tumor 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
11p partial monosomy syndrome Peritoneal multicystic mesothelioma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
11p partial monosomy syndrome Nephrogenic rest 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Peritoneal multicystic mesothelioma Wagner syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Wagner syndrome Wilms tumor 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Frasier syndrome Wagner syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Denys drash syndrome Wagner syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
11p partial monosomy syndrome Wagner syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
11p partial monosomy syndrome Ambiguous genitalia 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Ambiguous genitalia Denys drash syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Ambiguous genitalia Frasier syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Ambiguous genitalia Wilms tumor 1 0.167 1 3.23e-4 6.41e-4 ✓ sig.
11p partial monosomy syndrome Anus neoplasms 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Anus neoplasms Denys drash syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Anus neoplasms Frasier syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Anus neoplasms Wilms tumor 1 0.125 1 4.52e-4 8.26e-4 ✓ sig.
11p partial monosomy syndrome Peritoneal neoplasms 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Denys drash syndrome Peritoneal neoplasms 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Frasier syndrome Peritoneal neoplasms 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Peritoneal neoplasms Wilms tumor 1 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Peritoneal multicystic mesothelioma Peritoneal neoplasms 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Peritoneal neoplasms Tubulointerstitial kidney disease, autosomal dominant, 2 0.091 1 6.46e-4 1.09e-3 ✓ sig.
Cataract 30, pulverulent Peritoneal neoplasms 0.091 1 6.46e-4 1.09e-3 ✓ sig.