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 · 47 shared-gene connections
18 Diseases
77 Unique genes
0.255 Avg. similarity score
Acro-dermo-ungual-lacrimal-tooth syndrome Most-connected disease (12 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 ⇵
Acro-dermo-ungual-lacrimal-tooth syndrome 12 12 1
Ankyloblepharon-ectodermal defects-cleft lip/palate 12 12 1
Limb-mammary syndrome 10 10 1
Rudiger syndrome 9 9 1
Post-operative stroke 6 6 4
Sweat gland neoplasm 6 6 1
Bladder exstrophy 5 5 21
Breast disease 5 5 7
Cleft lip and cleft of alveolar process of maxilla 5 5 4
Congenital foot deformity 5 5 4
Omphalocele exstrophy imperforate anus 5 5 13
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 5 5 1
Bladder exstrophy and epispadias complex 3 3 27
Congenital hand deformities 2 2 8
Aarskog-scott syndrome, x-linked 1 1 1
BBS9-related ciliopathy 1 1 1
Cleft lip/palate-ectodermal dysplasia syndrome 1 1 1
fanconi anemia complementation group e 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TP63 14 / 18 Acro-dermo-ungual-lacrimal-tooth syndrome, Ankyloblepharon-ectodermal defects-cleft lip/palate, Bladder exstrophy, Bladder exstrophy and epispadias complex and 10 more
PTHLH 3 / 18 Breast disease, Congenital foot deformity, Congenital hand deformities
BBS9 2 / 18 BBS9-related ciliopathy, Post-operative stroke
FANCE 2 / 18 fanconi anemia complementation group e, Omphalocele exstrophy imperforate anus
FGD1 2 / 18 Aarskog-scott syndrome, x-linked, Congenital foot deformity
ISL1 2 / 18 Bladder exstrophy, Bladder exstrophy and epispadias complex
LMNA 2 / 18 Congenital foot deformity, Congenital hand deformities
NECTIN1 2 / 18 Cleft lip and cleft of alveolar process of maxilla, Cleft lip/palate-ectodermal dysplasia syndrome
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 ⇵
WNT ligand biogenesis and trafficking
WNT10A, WNT11, WNT3, WNT7A
 Reactome 4 / 25 25.0× 1.78e-5 5.44e-4 ✓ sig.
Basal cell carcinoma
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 63 12.4× 4.99e-5 1.28e-3 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 6 / 144 6.5× 3.15e-4 5.58e-3 ✓ sig.
Melanogenesis
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 101 7.7× 4.66e-4 7.55e-3 ✓ sig.
Cushing syndrome
CREB5, FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 6 / 155 6.0× 4.67e-4 7.56e-3 ✓ sig.
Hippo signaling pathway
FZD5, WNT10A, WNT11, WNT3, WNT7A, WWTR1
 KEGG 6 / 157 6.0× 5.00e-4 7.97e-3 ✓ sig.
mTOR signaling pathway
FZD5, WNT10A, WNT11, WNT3, WNT7A, FLCN
 KEGG 6 / 158 5.9× 5.18e-4 8.18e-3 ✓ sig.
Breast cancer
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 148 5.3× 2.57e-3 2.76e-2 ✓ sig.
Gastric cancer
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 150 5.2× 2.73e-3 2.88e-2 ✓ sig.
Hepatocellular carcinoma
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 170 4.6× 4.66e-3 4.18e-2 ✓ sig.
Wnt signaling pathway
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 174 4.5× 5.14e-3 4.45e-2 ✓ sig.
Defective CYP4F22 causes Ichthyosis, congenital, autosomal recessive 5 (ARCI5)
CYP4F22
 Reactome 1 / 1 156× 6.41e-3 5.16e-2
EPHA-mediated growth cone collapse
EFNA1, EPHA1
 Reactome 2 / 20 15.6× 7.15e-3 5.55e-2
EPH-Ephrin signaling
EFNA1, EPHA1
 Reactome 2 / 22 14.2× 8.63e-3 6.28e-2
Proteoglycans in cancer
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 204 3.8× 9.90e-3 6.82e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
canonical Wnt signaling pathway
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A, SOX9
 GO:0060070 7 / 105 16.2× 2.52e-7 2.63e-5 ✓ sig.
negative regulation of mesenchymal cell proliferation
ISL1, WNT11, LMNA
 GO:0072201 3 / 6 121× 1.33e-6 1.04e-4 ✓ sig.
stem cell proliferation
TP63, WNT11, WNT3, IRF6, SOX9
 GO:0072089 5 / 54 22.5× 2.81e-6 1.89e-4 ✓ sig.
embryonic hindlimb morphogenesis
TP63, WNT3, WNT7A, MSX1
 GO:0035116 4 / 29 33.5× 5.85e-6 3.40e-4 ✓ sig.
embryonic forelimb morphogenesis
TP63, WNT3, WNT7A, MSX1
 GO:0035115 4 / 33 29.4× 9.96e-6 5.20e-4 ✓ sig.
cell fate commitment
WNT10A, WNT11, WNT3, WNT7A, SOX9
 GO:0045165 5 / 75 16.2× 1.43e-5 6.93e-4 ✓ sig.
cloacal septation
TP63, WNT11
 GO:0060197 2 / 2 243× 1.68e-5 7.82e-4 ✓ sig.
mesenchymal cell proliferation
WNT11, MSX1, SOX9
 GO:0010463 3 / 16 45.5× 3.62e-5 1.41e-3 ✓ sig.
hair follicle development
TP63, SOX18, WNT10A, SOX9
 GO:0001942 4 / 48 20.2× 4.52e-5 1.67e-3 ✓ sig.
skin development
PKD1, WNT10A, IRF6, TFAP2B
 GO:0043588 4 / 55 17.7× 7.75e-5 2.50e-3 ✓ sig.
cartilage condensation
PKD1, WNT7A, SOX9
 GO:0001502 3 / 21 34.7× 8.48e-5 2.68e-3 ✓ sig.
regulation of cell adhesion
EPHA1, LMO7, PKD1, SOX9
 GO:0030155 4 / 61 15.9× 1.16e-4 3.39e-3 ✓ sig.
regulation of vesicle fusion
SYT1, SYT4
 GO:0031338 2 / 5 97.1× 1.66e-4 4.42e-3 ✓ sig.
cellular response to transforming growth factor beta stimulus
ISL1, WNT10A, WNT7A, SOX9
 GO:0071560 4 / 67 14.5× 1.68e-4 4.45e-3 ✓ sig.
animal organ morphogenesis
FGD1, TP63, PKD1, MSX1, PAX3
 GO:0009887 5 / 130 9.3× 2.00e-4 5.04e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital foot deformity Congenital hand deformities 0.300 3 3.68e-10 3.68e-9 ✓ sig.
Breast disease Congenital foot deformity 0.200 2 1.06e-6 6.56e-6 ✓ sig.
Breast disease Congenital hand deformities 0.143 2 4.95e-6 2.72e-5 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Ankyloblepharon-ectodermal defects-cleft lip/palate 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Rudiger syndrome Sweat gland neoplasm 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Limb-mammary syndrome Sweat gland neoplasm 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Limb-mammary syndrome Rudiger syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 Sweat gland neoplasm 0.500 1 6.49e-5 2.34e-4 ✓ sig.
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 Rudiger syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 Limb-mammary syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Rudiger syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Limb-mammary syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Sweat gland neoplasm 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Rudiger syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Sweat gland neoplasm 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Limb-mammary syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Aarskog-scott syndrome, x-linked Congenital foot deformity 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Post-operative stroke 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Post-operative stroke 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Limb-mammary syndrome Post-operative stroke 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Post-operative stroke Rudiger syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Post-operative stroke Sweat gland neoplasm 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Congenital foot deformity 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Congenital foot deformity 0.200 1 2.60e-4 6.40e-4 ✓ sig.
BBS9-related ciliopathy Post-operative stroke 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Rudiger syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Limb-mammary syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Cleft lip and cleft of alveolar process of maxilla 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Cleft lip and cleft of alveolar process of maxilla 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Cleft lip/palate-ectodermal dysplasia syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Breast disease Limb-mammary syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Breast disease 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Breast disease 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Bladder exstrophy Bladder exstrophy and epispadias complex 0.043 2 6.09e-4 1.18e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Omphalocele exstrophy imperforate anus Rudiger syndrome 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Limb-mammary syndrome Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.48e-3 ✓ sig.
fanconi anemia complementation group e Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Bladder exstrophy Rudiger syndrome 0.045 1 1.36e-3 2.13e-3 ✓ sig.
Bladder exstrophy Limb-mammary syndrome 0.045 1 1.36e-3 2.13e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Bladder exstrophy 0.045 1 1.36e-3 2.13e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Bladder exstrophy 0.045 1 1.36e-3 2.13e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Bladder exstrophy and epispadias complex 0.036 1 1.75e-3 2.59e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Bladder exstrophy and epispadias complex 0.036 1 1.75e-3 2.59e-3 ✓ sig.