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 28

20 diseases · 56 shared-gene connections
20 Diseases
68 Unique genes
0.263 Avg. similarity score
Acro-dermo-ungual-lacrimal-tooth syndrome Most-connected disease (13 links)
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Disease Searched: Muscular dystrophy, congenital, with or without seizures 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 13 13 1
Ankyloblepharon-ectodermal defects-cleft lip/palate 13 13 1
Limb-mammary syndrome 12 12 1
Rudiger syndrome 9 9 1
Bladder exstrophy 8 8 21
Rapp-hodgkin syndrome 8 8 1
Cleft lip/palate-ectodermal dysplasia syndrome 6 6 2
Bladder exstrophy and epispadias complex 5 5 27
Breast disease 5 5 7
Cleft lip and cleft of alveolar process of maxilla 5 5 4
Congenital foot deformity 5 5 4
Non-syndromic orofacial cleft type 8 5 5 1
Post-operative stroke 5 5 4
Sweat gland neoplasm 5 5 3
Congenital hand deformities 2 2 8
Zlotogora-ogur syndrome 2 2 1
Aarskog-scott syndrome, x-linked 1 1 1
Intellectual developmental disorder, autosomal recessive 65 1 1 1
Muscular dystrophy, congenital, with or without seizures 1 1 1
Vitreous body disease 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
TP63 15 / 20 Acro-dermo-ungual-lacrimal-tooth syndrome, Ankyloblepharon-ectodermal defects-cleft lip/palate, Bladder exstrophy, Bladder exstrophy and epispadias complex and 11 more
NECTIN1 3 / 20 Cleft lip and cleft of alveolar process of maxilla, Cleft lip/palate-ectodermal dysplasia syndrome, Zlotogora-ogur syndrome
PTHLH 3 / 20 Breast disease, Congenital foot deformity, Congenital hand deformities
FGD1 2 / 20 Aarskog-scott syndrome, x-linked, Congenital foot deformity
GOSR2 2 / 20 Bladder exstrophy, Muscular dystrophy, congenital, with or without seizures
ISL1 2 / 20 Bladder exstrophy, Bladder exstrophy and epispadias complex
KDM5B 2 / 20 Bladder exstrophy and epispadias complex, Intellectual developmental disorder, autosomal recessive 65
LMNA 2 / 20 Congenital foot deformity, Congenital hand deformities
NCKAP5 2 / 20 Bladder exstrophy, Vitreous body disease
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 28.3× 1.09e-5 3.12e-4 ✓ sig.
Basal cell carcinoma
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 63 14.0× 2.73e-5 6.73e-4 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 6 / 144 7.4× 1.59e-4 2.74e-3 ✓ sig.
Cushing syndrome
CREB5, FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 6 / 155 6.8× 2.37e-4 3.75e-3 ✓ sig.
Hippo signaling pathway
FZD5, WNT10A, WNT11, WNT3, WNT7A, WWTR1
 KEGG 6 / 157 6.7× 2.54e-4 3.97e-3 ✓ sig.
Melanogenesis
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 101 8.7× 2.61e-4 4.05e-3 ✓ sig.
Breast cancer
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 148 6.0× 1.48e-3 1.53e-2 ✓ sig.
Gastric cancer
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 150 5.9× 1.57e-3 1.60e-2 ✓ sig.
mTOR signaling pathway
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 158 5.6× 1.98e-3 1.89e-2 ✓ sig.
Hepatocellular carcinoma
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 170 5.2× 2.72e-3 2.38e-2 ✓ sig.
Wnt signaling pathway
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 174 5.1× 3.01e-3 2.54e-2 ✓ sig.
EPHA-mediated growth cone collapse
EFNA1, EPHA1
 Reactome 2 / 20 17.7× 5.62e-3 3.95e-2 ✓ sig.
Defective CYP4F22 causes Ichthyosis, congenital, autosomal recessive 5 (ARCI5)
CYP4F22
 Reactome 1 / 1 177× 5.66e-3 3.96e-2 ✓ sig.
Proteoglycans in cancer
FZD5, WNT10A, WNT11, WNT3, WNT7A
 KEGG 5 / 204 4.3× 5.90e-3 4.08e-2 ✓ sig.
EPH-Ephrin signaling
EFNA1, EPHA1
 Reactome 2 / 22 16.1× 6.78e-3 4.45e-2 ✓ 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 ⇵
canonical Wnt signaling pathway
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A, SOX9
 GO:0060070 7 / 105 18.3× 1.06e-7 1.33e-5 ✓ sig.
negative regulation of mesenchymal cell proliferation
ISL1, WNT11, LMNA
 GO:0072201 3 / 6 137× 9.15e-7 7.99e-5 ✓ sig.
stem cell proliferation
TP63, WNT11, WNT3, IRF6, SOX9
 GO:0072089 5 / 54 25.4× 1.51e-6 1.21e-4 ✓ sig.
embryonic hindlimb morphogenesis
TP63, WNT3, WNT7A, MSX1
 GO:0035116 4 / 29 37.9× 3.56e-6 2.41e-4 ✓ sig.
embryonic forelimb morphogenesis
TP63, WNT3, WNT7A, MSX1
 GO:0035115 4 / 33 33.3× 6.06e-6 3.69e-4 ✓ sig.
cell fate commitment
WNT10A, WNT11, WNT3, WNT7A, SOX9
 GO:0045165 5 / 75 18.3× 7.79e-6 4.50e-4 ✓ sig.
cloacal septation
TP63, WNT11
 GO:0060197 2 / 2 275× 1.30e-5 6.69e-4 ✓ sig.
Wnt signaling pathway
FZD5, PKD1, WNT10A, WNT11, WNT3, WNT7A, CYLD
 GO:0016055 7 / 232 8.3× 2.12e-5 9.66e-4 ✓ sig.
mesenchymal cell proliferation
WNT11, MSX1, SOX9
 GO:0010463 3 / 16 51.5× 2.49e-5 1.09e-3 ✓ sig.
hair follicle development
TP63, SOX18, WNT10A, SOX9
 GO:0001942 4 / 48 22.9× 2.77e-5 1.18e-3 ✓ sig.
skin development
PKD1, WNT10A, IRF6, TFAP2B
 GO:0043588 4 / 55 20.0× 4.76e-5 1.78e-3 ✓ sig.
cartilage condensation
PKD1, WNT7A, SOX9
 GO:0001502 3 / 21 39.3× 5.85e-5 2.08e-3 ✓ sig.
regulation of cell adhesion
EPHA1, LMO7, PKD1, SOX9
 GO:0030155 4 / 61 18.0× 7.16e-5 2.41e-3 ✓ sig.
cellular response to transforming growth factor beta stimulus
ISL1, WNT10A, WNT7A, SOX9
 GO:0071560 4 / 67 16.4× 1.03e-4 3.17e-3 ✓ sig.
animal organ morphogenesis
FGD1, TP63, PKD1, MSX1, PAX3
 GO:0009887 5 / 130 10.6× 1.11e-4 3.32e-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 3.62e-10 3.23e-9 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Cleft lip/palate-ectodermal dysplasia syndrome 0.400 2 5.00e-8 3.63e-7 ✓ sig.
Breast disease Congenital foot deformity 0.200 2 1.05e-6 6.38e-6 ✓ sig.
Breast disease Congenital hand deformities 0.143 2 4.90e-6 2.73e-5 ✓ sig.
Non-syndromic orofacial cleft type 8 Rapp-hodgkin syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Limb-mammary syndrome Rudiger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Limb-mammary syndrome Rapp-hodgkin syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Limb-mammary syndrome Non-syndromic orofacial cleft type 8 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Non-syndromic orofacial cleft type 8 Rudiger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Rapp-hodgkin syndrome Rudiger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Non-syndromic orofacial cleft type 8 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Rapp-hodgkin syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Rudiger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Limb-mammary syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Non-syndromic orofacial cleft type 8 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Rapp-hodgkin syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Rudiger syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Limb-mammary syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Ankyloblepharon-ectodermal defects-cleft lip/palate 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cleft lip/palate-ectodermal dysplasia syndrome Zlotogora-ogur syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Cleft lip/palate-ectodermal dysplasia syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cleft lip/palate-ectodermal dysplasia syndrome Rudiger syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Cleft lip/palate-ectodermal dysplasia syndrome Limb-mammary syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Cleft lip/palate-ectodermal dysplasia syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Rapp-hodgkin syndrome Sweat gland neoplasm 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Rudiger syndrome Sweat gland neoplasm 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Limb-mammary syndrome Sweat gland neoplasm 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Sweat gland neoplasm 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Sweat gland neoplasm 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Cleft lip and cleft of alveolar process of maxilla 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Zlotogora-ogur syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Post-operative stroke Rapp-hodgkin syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Post-operative stroke Rudiger syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Limb-mammary syndrome Post-operative stroke 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Post-operative stroke 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Post-operative stroke 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Cleft lip and cleft of alveolar process of maxilla 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Limb-mammary syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Aarskog-scott syndrome, x-linked Congenital foot deformity 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Congenital foot deformity 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Congenital foot deformity 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Breast disease Limb-mammary syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Breast disease 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Breast disease 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Bladder exstrophy Bladder exstrophy and epispadias complex 0.043 2 6.02e-4 1.04e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Bladder exstrophy 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Bladder exstrophy Limb-mammary syndrome 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Bladder exstrophy Rudiger syndrome 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Bladder exstrophy Muscular dystrophy, congenital, with or without seizures 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Bladder exstrophy Rapp-hodgkin syndrome 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Bladder exstrophy 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Bladder exstrophy and epispadias complex 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Bladder exstrophy and epispadias complex Limb-mammary syndrome 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Bladder exstrophy and epispadias complex Intellectual developmental disorder, autosomal recessive 65 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Bladder exstrophy and epispadias complex 0.036 1 1.74e-3 2.42e-3 ✓ sig.
Bladder exstrophy Vitreous body disease 0.043 1 2.71e-3 3.48e-3 ✓ sig.