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 142

11 diseases · 25 shared-gene connections
11 Diseases
14 Unique genes
0.307 Avg. similarity score
Atrioventricular septal defect Most-connected disease (6 links)
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Disease Searched: Holt-oram 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 ⇵
Atrioventricular septal defect 6 6 12
Chromosome 8p23.1 monosomy 6 6 1
Congenital pulmonary valve atresia 6 6 1
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 6 6 2
Partial atrioventricular canal defect 6 6 2
Testicular anomaly with congenital heart disease 6 6 1
Congenital heart disease with or without pancreatic hypoplasia or diabetes 5 5 1
Yorifuji okuno syndrome 5 5 4
Neurodevelopmental disorder with hypotonia and seizures 2 2 1
Holt-oram syndrome 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 / 11 Atrioventricular septal defect, Chromosome 8p23.1 monosomy, Congenital heart disease with or without pancreatic hypoplasia or diabetes, Congenital pulmonary valve atresia and 4 more
CRELD1 3 / 11 Atrioventricular septal defect, Neurodevelopmental disorder with hypotonia and seizures, Partial atrioventricular canal defect
GATA6 3 / 11 Atrioventricular septal defect, Pancreatic hypoplasia-diabetes-congenital heart disease syndrome, Yorifuji okuno syndrome
SMARCAL1 2 / 11 Atrioventricular septal defect, Schimke immuno-osseous dysplasia
TBX5 2 / 11 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 / 12 143× 8.27e-5 1.63e-3 ✓ sig.
YAP1- and WWTR1 (TAZ)-stimulated gene expression
GATA4, TBX5
 Reactome 2 / 14 123× 1.14e-4 2.10e-3 ✓ sig.
Regulation of gap junction activity
GJA1
 Reactome 1 / 3 286× 3.49e-3 2.83e-2 ✓ sig.
Beta oxidation of palmitoyl-CoA to myristoyl-CoA
ACADVL
 Reactome 1 / 3 286× 3.49e-3 2.83e-2 ✓ sig.
Factors involved in megakaryocyte development and platelet production
GATA4, GATA6
 Reactome 2 / 99 17.3× 5.74e-3 4.00e-2 ✓ sig.
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
GATA4
 Reactome 1 / 7 123× 8.13e-3 5.01e-2
RHO GTPases activate CIT
DLG4
 Reactome 1 / 8 107× 9.29e-3 5.43e-2
Formation of annular gap junctions
GJA1
 Reactome 1 / 11 78.0× 1.28e-2 6.57e-2
Gap junction degradation
GJA1
 Reactome 1 / 12 71.5× 1.39e-2 6.94e-2
Activation of Ca-permeable Kainate Receptor
DLG4
 Reactome 1 / 12 71.5× 1.39e-2 6.94e-2
cGMP-PKG signaling pathway
GATA4, MEF2C
 KEGG 2 / 166 10.3× 1.55e-2 7.40e-2
LGI-ADAM interactions
DLG4
 Reactome 1 / 14 61.3× 1.62e-2 7.59e-2
Trafficking of AMPA receptors
DLG4
 Reactome 1 / 17 50.5× 1.96e-2 8.49e-2
Transcriptional regulation of pluripotent stem cells
FOXP1
 Reactome 1 / 17 50.5× 1.96e-2 8.49e-2
Gap junction assembly
GJA1
 Reactome 1 / 18 47.7× 2.08e-2 8.77e-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 / 11 364× 5.50e-8 7.68e-6 ✓ sig.
endocardial cushion development
GATA4, TBX5, CRELD1
 GO:0003197 3 / 13 308× 9.53e-8 1.22e-5 ✓ sig.
cardiac muscle cell differentiation
GATA4, GATA6, TBX5
 GO:0055007 3 / 30 133× 1.34e-6 1.09e-4 ✓ sig.
positive regulation of cardiac muscle cell proliferation
GATA6, TBX5, MEF2C
 GO:0060045 3 / 32 125× 1.64e-6 1.29e-4 ✓ sig.
regulation of DNA-templated transcription
CHD7, FOXP1, GATA4, GATA6, NR1D2, TBX5, NR2F2, MEF2C
 GO:0006355 8 / 1,454 7.3× 2.59e-6 1.86e-4 ✓ sig.
NMDA selective glutamate receptor signaling pathway
MEF2C, DLG4
 GO:0098989 2 / 6 445× 7.80e-6 4.51e-4 ✓ sig.
atrioventricular node development
GATA4, GATA6
 GO:0003162 2 / 6 445× 7.80e-6 4.51e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
CHD7, GATA4, GATA6, NR1D2, TBX5, NR2F2, MEF2C
 GO:0045944 7 / 1,208 7.7× 1.06e-5 5.70e-4 ✓ sig.
positive regulation of DNA-templated transcription
GATA4, GATA6, NR1D2, TBX5, NR2F2, MEF2C
 GO:0045893 6 / 778 10.3× 1.15e-5 6.07e-4 ✓ sig.
sinoatrial node development
GATA6, TBX5
 GO:0003163 2 / 8 334× 1.46e-5 7.28e-4 ✓ sig.
skeletal muscle tissue development
ELN, NR2F2, MEF2C
 GO:0007519 3 / 68 58.9× 1.63e-5 7.92e-4 ✓ sig.
intestinal epithelial cell differentiation
GATA4, GATA6
 GO:0060575 2 / 11 243× 2.86e-5 1.20e-3 ✓ sig.
heart development
GATA4, TBX5, GJA1, MEF2C
 GO:0007507 4 / 273 19.6× 3.97e-5 1.55e-3 ✓ sig.
atrial septum morphogenesis
GATA4, TBX5
 GO:0060413 2 / 13 205× 4.05e-5 1.57e-3 ✓ sig.
negative regulation of transcription by RNA polymerase II
FOXP1, GATA4, GATA6, NR1D2, NR2F2, MEF2C
 GO:0000122 6 / 1,002 8.0× 4.85e-5 1.80e-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 5.00e-8 3.63e-7 ✓ sig.
Atrioventricular septal defect Partial atrioventricular canal defect 0.154 2 5.50e-7 3.46e-6 ✓ sig.
Atrioventricular septal defect Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.154 2 5.50e-7 3.46e-6 ✓ sig.
Atrioventricular septal defect Yorifuji okuno syndrome 0.133 2 3.30e-6 1.88e-5 ✓ sig.
Congenital pulmonary valve atresia Testicular anomaly with congenital heart disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital heart disease with or without pancreatic hypoplasia or diabetes Testicular anomaly with congenital heart disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Congenital heart disease with or without pancreatic hypoplasia or diabetes Congenital pulmonary valve atresia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome 8p23.1 monosomy Congenital heart disease with or without pancreatic hypoplasia or diabetes 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome 8p23.1 monosomy Congenital pulmonary valve atresia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome 8p23.1 monosomy Testicular anomaly with congenital heart disease 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome 8p23.1 monosomy Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Partial atrioventricular canal defect Testicular anomaly with congenital heart disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Pancreatic hypoplasia-diabetes-congenital heart disease syndrome Testicular anomaly with congenital heart disease 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurodevelopmental disorder with hypotonia and seizures Partial atrioventricular canal defect 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital pulmonary valve atresia Partial atrioventricular canal defect 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital pulmonary valve atresia Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital heart disease with or without pancreatic hypoplasia or diabetes Partial atrioventricular canal defect 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Congenital heart disease with or without pancreatic hypoplasia or diabetes Pancreatic hypoplasia-diabetes-congenital heart disease syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chromosome 8p23.1 monosomy Partial atrioventricular canal defect 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chromosome 8p23.1 monosomy Yorifuji okuno syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital pulmonary valve atresia Yorifuji okuno syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Testicular anomaly with congenital heart disease Yorifuji okuno syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Atrioventricular septal defect Holt-oram syndrome 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Atrioventricular septal defect Neurodevelopmental disorder with hypotonia and seizures 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Atrioventricular septal defect Schimke immuno-osseous dysplasia 0.077 1 7.75e-4 1.25e-3 ✓ sig.