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 33

18 diseases · 66 shared-gene connections
18 Diseases
15 Unique genes
0.413 Avg. similarity score
Cholestasis-pigmentary retinopathy-cleft palate syndrome Most-connected disease (15 links)
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Disease Searched: Opitz-kaveggia 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 ⇵
Cholestasis-pigmentary retinopathy-cleft palate syndrome 15 15 1
Disseminated peritoneal leiomyomatosis 15 15 1
Endometrial polyp 15 15 2
Uterine corpus epithelioid leiomyoma 15 15 1
Adenomyoma of uterine corpus 14 14 2
Simpson-golabi-behmel syndrome 6 6 5
Smooth muscle tumor 6 6 5
Fg syndrome 5 5 1
Fg syndrome 1 5 5 1
Granular cell tumor 5 5 3
Hardikar syndrome 5 5 1
Lujan-fryns syndrome 5 5 1
Ohdo syndrome, x-linked 5 5 1
Opitz-kaveggia syndrome 5 5 1
Uterine corpus undifferentiated sarcoma 5 5 2
Uterine corpus sarcoma 4 4 2
Nijmegen breakage syndrome 1 1 2
X-linked recessive hypoglycemia as part of simpson-golabi-behmel syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MED12 16 / 18 Adenomyoma of uterine corpus, Cholestasis-pigmentary retinopathy-cleft palate syndrome, Disseminated peritoneal leiomyomatosis, Endometrial polyp and 12 more
GPC3 2 / 18 Simpson-golabi-behmel syndrome, X-linked recessive hypoglycemia as part of simpson-golabi-behmel syndrome
NBN 2 / 18 Nijmegen breakage syndrome, Smooth muscle tumor
TP53 2 / 18 Smooth muscle tumor, Uterine corpus undifferentiated sarcoma
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 ⇵
Cellular senescence
NBN, RAD50, KRAS, TP53, PIK3CA
 KEGG 5 / 157 25.5× 9.68e-7 4.05e-5 ✓ sig.
Thyroid hormone signaling pathway
MED12, KRAS, TP53, PIK3CA
 KEGG 4 / 122 26.3× 1.27e-5 3.55e-4 ✓ sig.
Apoptosis
KRAS, TP53, PIK3CA, DAXX
 KEGG 4 / 137 23.4× 2.01e-5 5.23e-4 ✓ sig.
Sensing of DNA Double Strand Breaks
NBN, RAD50
 Reactome 2 / 6 267× 2.18e-5 5.59e-4 ✓ sig.
Hepatocellular carcinoma
KRAS, TP53, PIK3CA, SMARCA4
 KEGG 4 / 170 18.8× 4.68e-5 1.04e-3 ✓ sig.
Endometrial cancer
KRAS, TP53, PIK3CA
 KEGG 3 / 59 40.7× 4.91e-5 1.08e-3 ✓ sig.
HDR through MMEJ (alt-NHEJ)
NBN, RAD50
 Reactome 2 / 10 160× 6.51e-5 1.34e-3 ✓ sig.
Signaling by FGFR3 fusions in cancer
KRAS, PIK3CA
 Reactome 2 / 10 160× 6.51e-5 1.34e-3 ✓ sig.
DNA Damage/Telomere Stress Induced Senescence
NBN, RAD50, TP53
 Reactome 3 / 66 36.4× 6.88e-5 1.41e-3 ✓ sig.
Signaling by FGFR4 in disease
KRAS, PIK3CA
 Reactome 2 / 11 146× 7.96e-5 1.58e-3 ✓ sig.
Renal cell carcinoma
TFE3, KRAS, PIK3CA
 KEGG 3 / 70 34.3× 8.21e-5 1.62e-3 ✓ sig.
Transcriptional misregulation in cancer
TFE3, TP53, ASPSCR1, MEN1
 KEGG 4 / 198 16.2× 8.48e-5 1.67e-3 ✓ sig.
Central carbon metabolism in cancer
KRAS, TP53, PIK3CA
 KEGG 3 / 71 33.8× 8.56e-5 1.68e-3 ✓ sig.
Melanoma
KRAS, TP53, PIK3CA
 KEGG 3 / 73 32.9× 9.30e-5 1.80e-3 ✓ sig.
Non-small cell lung cancer
KRAS, TP53, PIK3CA
 KEGG 3 / 73 32.9× 9.30e-5 1.80e-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 ⇵
telomeric 3' overhang formation
NBN, RAD50
 GO:0031860 2 / 4 623× 3.61e-6 2.43e-4 ✓ sig.
transcription initiation-coupled chromatin remodeling
TP53, MEN1, SMARCA4
 GO:0045815 3 / 41 91.2× 4.38e-6 2.85e-4 ✓ sig.
negative regulation of telomere capping
NBN, RAD50
 GO:1904354 2 / 5 498× 6.01e-6 3.67e-4 ✓ sig.
positive regulation of double-strand break repair
NBN, RAD50, SMARCA4
 GO:2000781 3 / 47 79.5× 6.64e-6 3.96e-4 ✓ sig.
R-loop processing
NBN, RAD50
 GO:0062176 2 / 9 277× 2.16e-5 9.80e-4 ✓ sig.
homologous recombination
NBN, RAD50
 GO:0035825 2 / 12 208× 3.95e-5 1.54e-3 ✓ sig.
double-strand break repair
NBN, RAD50, TP53
 GO:0006302 3 / 87 43.0× 4.26e-5 1.63e-3 ✓ sig.
DNA strand resection involved in replication fork processing
NBN, RAD50
 GO:0110025 2 / 14 178× 5.44e-5 1.97e-3 ✓ sig.
DNA double-strand break processing
NBN, RAD50
 GO:0000729 2 / 15 166× 6.28e-5 2.19e-3 ✓ sig.
glial cell proliferation
KRAS, TP53
 GO:0014009 2 / 18 138× 9.13e-5 2.89e-3 ✓ sig.
positive regulation of cellular senescence
KRAS, TP53
 GO:2000774 2 / 20 125× 1.13e-4 3.39e-3 ✓ sig.
mitotic G2/M transition checkpoint
NBN, RAD50
 GO:0044818 2 / 21 119× 1.25e-4 3.63e-3 ✓ sig.
response to gamma radiation
TP53, MEN1
 GO:0010332 2 / 27 92.3× 2.09e-4 5.24e-3 ✓ sig.
positive regulation of DNA-templated transcription
MED12, TFE3, TP53, DAXX, SMARCA4
 GO:0045893 5 / 778 8.0× 2.62e-4 6.16e-3 ✓ sig.
positive regulation of telomere maintenance
NBN, RAD50
 GO:0032206 2 / 32 77.9× 2.94e-4 6.68e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cholestasis-pigmentary retinopathy-cleft palate syndrome Ohdo syndrome, x-linked 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Fg syndrome 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Hardikar syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Hardikar syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hardikar syndrome Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Hardikar syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Hardikar syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Lujan-fryns syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Lujan-fryns syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Lujan-fryns syndrome Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Lujan-fryns syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Lujan-fryns syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Disseminated peritoneal leiomyomatosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Ohdo syndrome, x-linked 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ohdo syndrome, x-linked Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Ohdo syndrome, x-linked 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Ohdo syndrome, x-linked 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Opitz-kaveggia syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Opitz-kaveggia syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Opitz-kaveggia syndrome Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Opitz-kaveggia syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Opitz-kaveggia syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Uterine corpus epithelioid leiomyoma Uterine corpus undifferentiated sarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Fg syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Endometrial polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Uterine corpus undifferentiated sarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Disseminated peritoneal leiomyomatosis 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Endometrial polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Uterine corpus undifferentiated sarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Endometrial polyp 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Uterine corpus undifferentiated sarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Cholestasis-pigmentary retinopathy-cleft palate syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Uterine corpus undifferentiated sarcoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Fg syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Fg syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Adenomyoma of uterine corpus Fg syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Fg syndrome 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Fg syndrome 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Fg syndrome 1 Uterine corpus epithelioid leiomyoma 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Endometrial polyp Fg syndrome 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Uterine corpus sarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Uterine corpus sarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Uterine corpus epithelioid leiomyoma Uterine corpus sarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Endometrial polyp Uterine corpus sarcoma 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Granular cell tumor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Adenomyoma of uterine corpus Granular cell tumor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Endometrial polyp Granular cell tumor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Granular cell tumor Uterine corpus epithelioid leiomyoma 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Granular cell tumor 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Smooth muscle tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Smooth muscle tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Smooth muscle tumor Uterine corpus epithelioid leiomyoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Endometrial polyp Smooth muscle tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Adenomyoma of uterine corpus Smooth muscle tumor 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cholestasis-pigmentary retinopathy-cleft palate syndrome Simpson-golabi-behmel syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Disseminated peritoneal leiomyomatosis Simpson-golabi-behmel syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Simpson-golabi-behmel syndrome Uterine corpus epithelioid leiomyoma 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Endometrial polyp Simpson-golabi-behmel syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Adenomyoma of uterine corpus Simpson-golabi-behmel syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Simpson-golabi-behmel syndrome X-linked recessive hypoglycemia as part of simpson-golabi-behmel syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Nijmegen breakage syndrome Smooth muscle tumor 0.167 1 5.16e-4 9.13e-4 ✓ sig.