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 57

15 diseases · 31 shared-gene connections
15 Diseases
39 Unique genes
0.268 Avg. similarity score
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome Most-connected disease (7 links)
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Disease Searched: Atrioventricular septal defect 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 ⇵
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 7 7 2
Yorifuji okuno syndrome 7 7 4
Atrioventricular septal defect 6 6 12
Chromosome 8p23.1 monosomy 6 6 1
Congenital pulmonary valve atresia 6 6 1
Partial atrioventricular canal defect 6 6 2
Testicular anomaly with congenital heart disease 6 6 1
GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes 5 5 1
Very long chain acyl-coa dehydrogenase deficiency 3 3 4
Vulto-van silfhout-de vries syndrome 3 3 2
Williams syndrome 3 3 24
Brain abnormalities developmental delay facial dysmorphism intellectual disability syndrome 1 1 1
holt-oram syndrome 1 1 1
leber-like hereditary optic neuropathy, autosomal recessive 1 1 1 1
schimke immuno-osseous dysplasia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GATA4 8 / 15 Atrioventricular septal defect, Chromosome 8p23.1 monosomy, Congenital pulmonary valve atresia, GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes and 4 more
DLG4 4 / 15 Very long chain acyl-coa dehydrogenase deficiency, Vulto-van silfhout-de vries syndrome, Williams syndrome, Yorifuji okuno syndrome
GATA6 3 / 15 Atrioventricular septal defect, Pancreatic hypoplasia-diabetes-congenital heart disease syndrome, Yorifuji okuno syndrome
ACADVL 2 / 15 Very long chain acyl-coa dehydrogenase deficiency, Yorifuji okuno syndrome
CRELD1 2 / 15 Atrioventricular septal defect, Partial atrioventricular canal defect
DNAJC30 2 / 15 leber-like hereditary optic neuropathy, autosomal recessive 1, Williams syndrome
ELN 2 / 15 Atrioventricular septal defect, Williams syndrome
MEF2C 2 / 15 Atrioventricular septal defect, Brain abnormalities developmental delay facial dysmorphism intellectual disability syndrome
SMARCAL1 2 / 15 Atrioventricular septal defect, schimke immuno-osseous dysplasia
TBX5 2 / 15 Atrioventricular septal defect, holt-oram 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 ⇵
Physiological factors
GATA4, TBX5
 Reactome 2 / 12 51.3× 6.64e-4 9.82e-3 ✓ sig.
LGI-ADAM interactions
DLG4, STX1A
 Reactome 2 / 14 44.0× 9.12e-4 1.25e-2 ✓ sig.
YAP1- and WWTR1 (TAZ)-stimulated gene expression
GATA4, TBX5
 Reactome 2 / 14 44.0× 9.12e-4 1.25e-2 ✓ sig.
PCP/CE pathway
DVL2, FZD3
 Reactome 2 / 18 34.2× 1.52e-3 1.86e-2 ✓ sig.
PKA-mediated phosphorylation of key metabolic factors
MLXIPL
 Reactome 1 / 1 308× 3.25e-3 3.24e-2 ✓ sig.
Fatty acid degradation
ACADL, ACADVL
 KEGG 2 / 43 14.3× 8.53e-3 6.26e-2
Toxicity of botulinum toxin type C (BoNT/C)
STX1A
 Reactome 1 / 3 103× 9.71e-3 6.81e-2
Regulation of gap junction activity
GJA1
 Reactome 1 / 3 103× 9.71e-3 6.81e-2
Beta oxidation of myristoyl-CoA to lauroyl-CoA
ACADL
 Reactome 1 / 3 103× 9.71e-3 6.81e-2
Beta oxidation of palmitoyl-CoA to myristoyl-CoA
ACADVL
 Reactome 1 / 3 103× 9.71e-3 6.81e-2
Hippo signaling pathway
DLG4, DVL2, FZD3
 KEGG 3 / 157 5.9× 1.42e-2 8.57e-2
Fatty acid metabolism
ACADL, ACADVL
 KEGG 2 / 57 10.8× 1.47e-2 8.74e-2
Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA
ACADL
 Reactome 1 / 5 61.6× 1.61e-2 9.30e-2
cGMP-PKG signaling pathway
GATA4, MEF2C, GTF2I
 KEGG 3 / 166 5.6× 1.65e-2 9.40e-2
Asymmetric localization of PCP proteins
DVL2, FZD3
 Reactome 2 / 62 9.9× 1.72e-2 9.65e-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 ⇵
atrioventricular canal development
CHD7, GATA4, GATA6
 GO:0036302 3 / 11 131× 1.37e-6 1.07e-4 ✓ sig.
endocardial cushion development
GATA4, TBX5, CRELD1
 GO:0003197 3 / 13 111× 2.37e-6 1.66e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
CHD7, GATA4, GATA6, NR1D2, TBX5, MEF2C, NR2F2, DVL2, BAZ1B, GTF2I, MLXIPL
 GO:0045944 11 / 1,208 4.4× 2.45e-5 1.05e-3 ✓ sig.
cardiac muscle cell differentiation
GATA4, GATA6, TBX5
 GO:0055007 3 / 30 47.9× 3.28e-5 1.31e-3 ✓ sig.
positive regulation of cardiac muscle cell proliferation
GATA6, TBX5, MEF2C
 GO:0060045 3 / 32 44.9× 4.00e-5 1.53e-3 ✓ sig.
NMDA selective glutamate receptor signaling pathway
MEF2C, DLG4
 GO:0098989 2 / 6 160× 6.33e-5 2.16e-3 ✓ sig.
atrioventricular node development
GATA4, GATA6
 GO:0003162 2 / 6 160× 6.33e-5 2.16e-3 ✓ sig.
sinoatrial node development
GATA6, TBX5
 GO:0003163 2 / 8 120× 1.18e-4 3.43e-3 ✓ sig.
positive regulation of neuron projection arborization
DLG4, DVL2
 GO:0150012 2 / 8 120× 1.18e-4 3.43e-3 ✓ sig.
regulation of DNA-templated transcription
CHD7, FOXP1, GATA4, GATA6, NR1D2, TBX5, MEF2C, NR2F2, DVL2, GTF2IRD1, MLXIPL
 GO:0006355 11 / 1,454 3.6× 1.33e-4 3.75e-3 ✓ sig.
positive regulation of DNA-templated transcription
GATA4, GATA6, NR1D2, TBX5, MEF2C, NR2F2, DEAF1, MLXIPL
 GO:0045893 8 / 778 4.9× 1.70e-4 4.51e-3 ✓ sig.
negative regulation of transcription by RNA polymerase II
FOXP1, GATA4, GATA6, NR1D2, MEF2C, NR2F2, DEAF1, GTF2IRD1, MLXIPL
 GO:0000122 9 / 1,002 4.3× 1.74e-4 4.59e-3 ✓ sig.
negative regulation of fatty acid oxidation
ACADL, ACADVL
 GO:0046322 2 / 10 95.8× 1.89e-4 4.87e-3 ✓ sig.
transcription by RNA polymerase II
CHD7, TBX5, DEAF1, GTF2I, GTF2IRD1
 GO:0006366 5 / 261 9.2× 2.00e-4 5.05e-3 ✓ sig.
intestinal epithelial cell differentiation
GATA4, GATA6
 GO:0060575 2 / 11 87.1× 2.31e-4 5.57e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome Yorifuji okuno syndrome 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Very long chain acyl-coa dehydrogenase deficiency Yorifuji okuno syndrome 0.286 2 3.04e-7 1.95e-6 ✓ sig.
Atrioventricular septal defect Partial atrioventricular canal defect 0.154 2 5.57e-7 3.41e-6 ✓ sig.
Atrioventricular septal defect Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.154 2 5.57e-7 3.41e-6 ✓ sig.
Atrioventricular septal defect Yorifuji okuno syndrome 0.133 2 3.34e-6 1.79e-5 ✓ sig.
Chromosome 8p23.1 monosomy Congenital pulmonary valve atresia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Chromosome 8p23.1 monosomy Testicular anomaly with congenital heart disease 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Chromosome 8p23.1 monosomy GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital pulmonary valve atresia Testicular anomaly with congenital heart disease 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Congenital pulmonary valve atresia GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes 0.500 1 6.49e-5 2.33e-4 ✓ sig.
GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes Testicular anomaly with congenital heart disease 0.500 1 6.49e-5 2.33e-4 ✓ sig.
GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes Partial atrioventricular canal defect 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Partial atrioventricular canal defect Testicular anomaly with congenital heart disease 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome Testicular anomaly with congenital heart disease 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital pulmonary valve atresia Partial atrioventricular canal defect 0.333 1 1.30e-4 3.93e-4 ✓ sig.
GATA4-related congenital heart disease with or without pancreatic hypoplasia or diabetes Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital pulmonary valve atresia Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Chromosome 8p23.1 monosomy Partial atrioventricular canal defect 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Chromosome 8p23.1 monosomy Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome Partial atrioventricular canal defect 0.250 1 2.60e-4 6.51e-4 ✓ sig.
Testicular anomaly with congenital heart disease Yorifuji okuno syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Congenital pulmonary valve atresia Yorifuji okuno syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Chromosome 8p23.1 monosomy Yorifuji okuno syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Very long chain acyl-coa dehydrogenase deficiency Vulto-van silfhout-de vries syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Vulto-van silfhout-de vries syndrome Yorifuji okuno syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Atrioventricular septal defect Brain abnormalities developmental delay facial dysmorphism intellectual disability syndrome 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Atrioventricular septal defect schimke immuno-osseous dysplasia 0.077 1 7.79e-4 1.40e-3 ✓ sig.
Atrioventricular septal defect holt-oram syndrome 0.077 1 7.79e-4 1.40e-3 ✓ sig.
leber-like hereditary optic neuropathy, autosomal recessive 1 Williams syndrome 0.040 1 1.56e-3 2.38e-3 ✓ sig.
Vulto-van silfhout-de vries syndrome Williams syndrome 0.038 1 3.11e-3 4.09e-3 ✓ sig.
Very long chain acyl-coa dehydrogenase deficiency Williams syndrome 0.036 1 6.22e-3 7.47e-3 ✓ sig.