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 390

6 diseases · 14 shared-gene connections
6 Diseases
10 Unique genes
0.284 Avg. similarity score
Chromosome 22q11.2 microduplication syndrome Most-connected disease (5 links)
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Disease Searched: Conotruncal heart malformations 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 ⇵
Chromosome 22q11.2 microduplication syndrome 5 5 1
Common arterial trunk with aortic dominance 5 5 2
Common arterial trunk with pulmonary dominance and interrupted aortic arch 5 5 2
Conotruncal anomaly face syndrome 5 5 1
Conotruncal heart malformations 4 4 6
Velocardiofacial syndrome 4 4 5

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

Gene ⇵ Member diseases ⇵ Linked diseases
TBX1 6 / 6 Chromosome 22q11.2 microduplication syndrome, Common arterial trunk with aortic dominance, Common arterial trunk with pulmonary dominance and interrupted aortic arch, Conotruncal anomaly face syndrome and 2 more
GATA6 3 / 6 Common arterial trunk with aortic dominance, Common arterial trunk with pulmonary dominance and interrupted aortic arch, Conotruncal heart malformations
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 ⇵
Factors involved in megakaryocyte development and platelet production
GATA6, ZFPM2
 Reactome 2 / 99 24.3× 2.90e-3 2.49e-2 ✓ sig.
Physiological factors
NKX2-5
 Reactome 1 / 12 100× 9.95e-3 5.67e-2
YAP1- and WWTR1 (TAZ)-stimulated gene expression
NKX2-5
 Reactome 1 / 14 85.8× 1.16e-2 6.22e-2
MicroRNA (miRNA) biogenesis
DGCR8
 Reactome 1 / 24 50.0× 1.98e-2 8.52e-2
Surfactant metabolism
GATA6
 Reactome 1 / 29 41.4× 2.39e-2 9.49e-2
Cytokine-cytokine receptor interaction
GDF1
 KEGG 1 / 298 4.0× 2.22e-1 3.54e-1
MicroRNAs in cancer
ZFPM2
 KEGG 1 / 311 3.9× 2.31e-1 3.63e-1

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
outflow tract septum morphogenesis
TBX1, GATA6, ZFPM2, NKX2-5
 GO:0003148 4 / 28 267× 8.41e-10 2.00e-7 ✓ sig.
pharyngeal system development
TBX1, NKX2-6, NKX2-5
 GO:0060037 3 / 21 267× 1.46e-7 1.75e-5 ✓ sig.
cardiac muscle tissue development
GATA6, ZFPM2, NKX2-5
 GO:0048738 3 / 24 234× 2.22e-7 2.47e-5 ✓ sig.
epithelial cell differentiation
TBX1, GATA6, NKX2-6, NKX2-5
 GO:0030855 4 / 110 68.0× 2.32e-7 2.56e-5 ✓ sig.
right ventricular cardiac muscle tissue morphogenesis
ZFPM2, NKX2-5
 GO:0003221 2 / 2 1,869× 2.58e-7 2.79e-5 ✓ sig.
atrial cardiac muscle cell development
NKX2-6, NKX2-5
 GO:0055014 2 / 3 1,246× 7.73e-7 6.94e-5 ✓ sig.
atrioventricular node development
GATA6, NKX2-5
 GO:0003162 2 / 6 623× 3.86e-6 2.57e-4 ✓ sig.
outflow tract morphogenesis
TBX1, ZFPM2, NKX2-5
 GO:0003151 3 / 63 89.0× 4.31e-6 2.81e-4 ✓ sig.
positive regulation of epithelial cell proliferation
TBX1, NKX2-6, NKX2-5
 GO:0050679 3 / 73 76.8× 6.73e-6 4.00e-4 ✓ sig.
heart development
TBX1, ZFPM2, NKX2-6, NKX2-5
 GO:0007507 4 / 273 27.4× 8.73e-6 4.90e-4 ✓ sig.
ventricular cardiac muscle cell development
NKX2-6, NKX2-5
 GO:0055015 2 / 11 340× 1.41e-5 7.12e-4 ✓ sig.
cardiac muscle tissue morphogenesis
ZFPM2, NKX2-5
 GO:0055008 2 / 13 287× 2.00e-5 9.25e-4 ✓ sig.
negative regulation of epithelial cell apoptotic process
NKX2-6, NKX2-5
 GO:1904036 2 / 16 234× 3.08e-5 1.28e-3 ✓ sig.
epithelial cell apoptotic process
NKX2-6, NKX2-5
 GO:1904019 2 / 20 187× 4.87e-5 1.81e-3 ✓ sig.
heart contraction
GATA6, NKX2-5
 GO:0060047 2 / 23 162× 6.48e-5 2.24e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Common arterial trunk with aortic dominance Common arterial trunk with pulmonary dominance and interrupted aortic arch 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Common arterial trunk with aortic dominance Conotruncal heart malformations 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Common arterial trunk with pulmonary dominance and interrupted aortic arch Conotruncal heart malformations 0.286 2 1.25e-7 8.63e-7 ✓ sig.
Chromosome 22q11.2 microduplication syndrome Conotruncal anomaly face syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome 22q11.2 microduplication syndrome Common arterial trunk with aortic dominance 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chromosome 22q11.2 microduplication syndrome Common arterial trunk with pulmonary dominance and interrupted aortic arch 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Common arterial trunk with aortic dominance Conotruncal anomaly face syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Common arterial trunk with pulmonary dominance and interrupted aortic arch Conotruncal anomaly face syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chromosome 22q11.2 microduplication syndrome Velocardiofacial syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Conotruncal anomaly face syndrome Velocardiofacial syndrome 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Chromosome 22q11.2 microduplication syndrome Conotruncal heart malformations 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Conotruncal anomaly face syndrome Conotruncal heart malformations 0.143 1 3.87e-4 7.33e-4 ✓ sig.
Common arterial trunk with aortic dominance Velocardiofacial syndrome 0.143 1 6.46e-4 1.09e-3 ✓ sig.
Common arterial trunk with pulmonary dominance and interrupted aortic arch Velocardiofacial syndrome 0.143 1 6.46e-4 1.09e-3 ✓ sig.