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 23

19 diseases · 47 shared-gene connections
19 Diseases
114 Unique genes
0.210 Avg. similarity score
Acro-dermo-ungual-lacrimal-tooth syndrome Most-connected disease (11 links)
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Disease Searched: fanconi anemia complementation group e 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 11 11 1
Ankyloblepharon-ectodermal defects-cleft lip/palate 11 11 1
Limb-mammary syndrome 9 9 1
Rudiger syndrome 8 8 1
Sweat gland neoplasm 7 7 1
Cleft lip and cleft of alveolar process of maxilla 6 6 4
Congenital foot deformity 6 6 4
Omphalocele exstrophy imperforate anus 6 6 13
Post-operative stroke 6 6 4
Bladder exstrophy 5 5 21
Breast disease 5 5 7
Bladder exstrophy and epispadias complex 3 3 27
Growth disorder 3 3 35
Aarskog-scott syndrome, x-linked 2 2 1
Congenital hand deformities 2 2 8
BBS9-related ciliopathy 1 1 1
Cleft lip/palate-ectodermal dysplasia syndrome 1 1 1
Tessadori-van haaften neurodevelopmental syndrome 1 1 6
fanconi anemia complementation group e 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TP63 13 / 19 Acro-dermo-ungual-lacrimal-tooth syndrome, Ankyloblepharon-ectodermal defects-cleft lip/palate, Bladder exstrophy, Bladder exstrophy and epispadias complex and 9 more
PTHLH 4 / 19 Breast disease, Congenital foot deformity, Congenital hand deformities, Growth disorder
FGD1 3 / 19 Aarskog-scott syndrome, x-linked, Congenital foot deformity, Growth disorder
ADAMTSL2 2 / 19 Congenital hand deformities, Growth disorder
BBS9 2 / 19 BBS9-related ciliopathy, Post-operative stroke
FANCE 2 / 19 fanconi anemia complementation group e, Omphalocele exstrophy imperforate anus
H4C3 2 / 19 Growth disorder, Tessadori-van haaften neurodevelopmental syndrome
ISL1 2 / 19 Bladder exstrophy, Bladder exstrophy and epispadias complex
LMNA 2 / 19 Congenital foot deformity, Congenital hand deformities
NECTIN1 2 / 19 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 ⇵
Packaging Of Telomere Ends
H4C3, TINF2, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 52 14.2× 5.42e-7 2.87e-5 ✓ sig.
Recognition and association of DNA glycosylase with site containing an affected purine
H4C3, TINF2, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 56 13.2× 9.11e-7 4.48e-5 ✓ sig.
Cleavage of the damaged purine
H4C3, TINF2, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 56 13.2× 9.11e-7 4.48e-5 ✓ sig.
DNA Damage/Telomere Stress Induced Senescence
H4C3, TINF2, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 66 11.2× 2.83e-6 1.20e-4 ✓ sig.
PRC2 methylates histones and DNA
DNMT3A, H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 73 10.1× 5.61e-6 2.13e-4 ✓ sig.
HDMs demethylate histones
KDM5B, H4C3, H4C1, H4C11, H4C5, H4C9
 Reactome 6 / 50 12.6× 7.25e-6 2.63e-4 ✓ sig.
NoRC negatively regulates rRNA expression
H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 6 / 61 10.4× 2.33e-5 6.91e-4 ✓ sig.
B-WICH complex positively regulates rRNA expression
ERCC6, H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 91 8.1× 2.42e-5 7.15e-4 ✓ sig.
HATs acetylate histones
PAX3, H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 7 / 93 7.9× 2.79e-5 8.01e-4 ✓ sig.
SIRT1 negatively regulates rRNA expression
H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 6 / 63 10.0× 2.80e-5 8.04e-4 ✓ sig.
RNA Polymerase I Promoter Opening
H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 6 / 63 10.0× 2.80e-5 8.04e-4 ✓ sig.
Hepatocellular carcinoma
FZD5, WNT10A, WNT11, WNT3, WNT7A, HMOX1, IGF1R, IGF2, PIK3CA
 KEGG 9 / 170 5.6× 3.35e-5 9.30e-4 ✓ sig.
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 6 / 67 9.4× 3.99e-5 1.08e-3 ✓ sig.
Nonhomologous End-Joining (NHEJ)
H4C3, H4C1, H4C11, H4C5, H2BC12, H4C9
 Reactome 6 / 69 9.2× 4.72e-5 1.24e-3 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A, IGF1R, PIK3CA
 KEGG 8 / 144 5.9× 6.63e-5 1.63e-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 ⇵
protein localization to CENP-A containing chromatin
H4C3, H4C1, H4C11, H4C5, H4C9
 GO:0061644 5 / 18 45.5× 6.22e-8 8.15e-6 ✓ sig.
negative regulation of megakaryocyte differentiation
H4C3, H4C1, H4C11, H4C5, H4C9
 GO:0045653 5 / 20 41.0× 1.11e-7 1.34e-5 ✓ sig.
telomere organization
H4C3, H4C1, H4C11, H4C5, H4C9
 GO:0032200 5 / 28 29.3× 6.80e-7 6.09e-5 ✓ sig.
canonical Wnt signaling pathway
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A, SOX9
 GO:0060070 7 / 105 10.9× 3.63e-6 2.37e-4 ✓ sig.
negative regulation of mesenchymal cell proliferation
ISL1, WNT11, LMNA
 GO:0072201 3 / 6 82.0× 4.36e-6 2.74e-4 ✓ sig.
nucleosome assembly
SOX9, ATRX, H4C3, H4C1, H4C11, H4C5, H4C9
 GO:0006334 7 / 119 9.6× 8.33e-6 4.62e-4 ✓ sig.
stem cell proliferation
TP63, WNT11, WNT3, IRF6, SOX9
 GO:0072089 5 / 54 15.2× 1.93e-5 8.85e-4 ✓ sig.
skin development
PKD1, WNT10A, IRF6, TFAP2B, ATP7A
 GO:0043588 5 / 55 14.9× 2.11e-5 9.50e-4 ✓ sig.
embryonic hindlimb morphogenesis
TP63, WNT3, WNT7A, MSX1
 GO:0035116 4 / 29 22.6× 2.77e-5 1.17e-3 ✓ sig.
cloacal septation
TP63, WNT11
 GO:0060197 2 / 2 164× 3.69e-5 1.46e-3 ✓ sig.
cellular response to glycoprotein
TSHR, NPPC
 GO:1904588 2 / 2 164× 3.69e-5 1.46e-3 ✓ sig.
embryonic forelimb morphogenesis
TP63, WNT3, WNT7A, MSX1
 GO:0035115 4 / 33 19.9× 4.69e-5 1.75e-3 ✓ sig.
angiogenesis
EFNA1, NUS1, EPHA1, FZD5, SOX18, WNT7A, HMOX1, NPPC, PIK3CA
 GO:0001525 9 / 284 5.2× 6.13e-5 2.14e-3 ✓ sig.
neuron differentiation
ISL1, FZD5, WNT10A, WNT11, WNT3, WNT7A, DNMT3A, ERCC6
 GO:0030182 8 / 222 5.9× 6.54e-5 2.24e-3 ✓ sig.
blood vessel development
ANTXR1, PKD1, SOX18, AHR, ATP7A
 GO:0001568 5 / 70 11.7× 6.83e-5 2.32e-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 3.68e-10 3.50e-9 ✓ sig.
Breast disease Congenital foot deformity 0.200 2 1.06e-6 6.23e-6 ✓ sig.
Breast disease Congenital hand deformities 0.143 2 4.95e-6 2.58e-5 ✓ sig.
Congenital foot deformity Growth disorder 0.053 2 3.00e-5 1.39e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Sweat gland neoplasm 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Limb-mammary syndrome Rudiger syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Limb-mammary syndrome Sweat gland neoplasm 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Rudiger syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Limb-mammary syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Rudiger syndrome Sweat gland neoplasm 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Sweat gland neoplasm 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Rudiger syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Limb-mammary syndrome 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Ankyloblepharon-ectodermal defects-cleft lip/palate 0.500 1 6.49e-5 2.32e-4 ✓ sig.
Limb-mammary syndrome Post-operative stroke 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Cleft lip/palate-ectodermal dysplasia syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Congenital foot deformity 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Rudiger syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Congenital foot deformity 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Post-operative stroke 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Post-operative stroke 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Aarskog-scott syndrome, x-linked Congenital foot deformity 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Post-operative stroke Rudiger syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Post-operative stroke Sweat gland neoplasm 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Sweat gland neoplasm 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Cleft lip and cleft of alveolar process of maxilla 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Cleft lip and cleft of alveolar process of maxilla 0.200 1 2.60e-4 6.48e-4 ✓ sig.
BBS9-related ciliopathy Post-operative stroke 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Cleft lip and cleft of alveolar process of maxilla Limb-mammary syndrome 0.200 1 2.60e-4 6.48e-4 ✓ sig.
Breast disease Limb-mammary syndrome 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Breast disease 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Breast disease 0.125 1 4.55e-4 9.70e-4 ✓ sig.
Bladder exstrophy Bladder exstrophy and epispadias complex 0.043 2 6.09e-4 1.20e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Omphalocele exstrophy imperforate anus Sweat gland neoplasm 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Omphalocele exstrophy imperforate anus Rudiger syndrome 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Limb-mammary syndrome Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.50e-3 ✓ sig.
fanconi anemia complementation group e Omphalocele exstrophy imperforate anus 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Bladder exstrophy Rudiger syndrome 0.045 1 1.36e-3 2.15e-3 ✓ sig.
Bladder exstrophy Limb-mammary syndrome 0.045 1 1.36e-3 2.15e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Bladder exstrophy 0.045 1 1.36e-3 2.15e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Bladder exstrophy 0.045 1 1.36e-3 2.15e-3 ✓ sig.
Acro-dermo-ungual-lacrimal-tooth syndrome Bladder exstrophy and epispadias complex 0.036 1 1.75e-3 2.61e-3 ✓ sig.
Ankyloblepharon-ectodermal defects-cleft lip/palate Bladder exstrophy and epispadias complex 0.036 1 1.75e-3 2.61e-3 ✓ sig.
Aarskog-scott syndrome, x-linked Growth disorder 0.028 1 2.27e-3 3.19e-3 ✓ sig.
Growth disorder Tessadori-van haaften neurodevelopmental syndrome 0.024 1 1.36e-2 1.51e-2 ✓ sig.