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 472

6 diseases · 7 shared-gene connections
6 Diseases
6 Unique genes
0.264 Avg. similarity score
Congenital heart disease with or without pancreatic agenesis or neonatal diabetes Most-connected disease (3 links)
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Disease 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 ⇵
Congenital heart disease with or without pancreatic agenesis or neonatal diabetes 3 3 1
Pancreatic agenesis, diaphragmatic hernia, and congenital heart defects 3 3 1
Partial pancreatic agenesis 3 3 4
Truncus arteriosus 3 3 3
Cardiac malformation syndrome 1 1 1
Pancreatic beta-cell agenesis with neonatal diabetes mellitus 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GATA6 4 / 6 Congenital heart disease with or without pancreatic agenesis or neonatal diabetes, Pancreatic agenesis, diaphragmatic hernia, and congenital heart defects, Partial pancreatic agenesis, Truncus arteriosus
PLXND1 2 / 6 Cardiac malformation syndrome, Truncus arteriosus
PTF1A 2 / 6 Pancreatic beta-cell agenesis with neonatal diabetes mellitus, Partial pancreatic agenesis
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 ⇵
Other semaphorin interactions
PLXND1
 Reactome 1 / 14 143× 6.98e-3 4.53e-2 ✓ sig.
NOTCH3 Intracellular Domain Regulates Transcription
PLXND1
 Reactome 1 / 18 111× 8.96e-3 5.31e-2
Maturity onset diabetes of the young
PDX1
 KEGG 1 / 26 77.0× 1.29e-2 6.62e-2
Surfactant metabolism
GATA6
 Reactome 1 / 29 69.0× 1.44e-2 7.09e-2
Type II diabetes mellitus
PDX1
 KEGG 1 / 47 42.6× 2.33e-2 9.35e-2
Insulin secretion
PDX1
 KEGG 1 / 86 23.3× 4.22e-2 1.31e-1
Factors involved in megakaryocyte development and platelet production
GATA6
 Reactome 1 / 99 20.2× 4.85e-2 1.42e-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 ⇵
pancreas development
PTF1A, GATA6, PDX1, ZNF808
 GO:0031016 4 / 30 415× 8.08e-11 2.52e-8 ✓ sig.
exocrine pancreas development
PTF1A, PDX1
 GO:0031017 2 / 10 623× 3.86e-6 2.57e-4 ✓ sig.
type B pancreatic cell differentiation
GATA6, PDX1
 GO:0003309 2 / 10 623× 3.86e-6 2.57e-4 ✓ sig.
cell differentiation
PTF1A, GATA6, PDX1, ZNF808
 GO:0030154 4 / 1,051 11.9× 1.36e-4 3.85e-3 ✓ sig.
stem cell differentiation
GATA6, PDX1
 GO:0048863 2 / 63 98.9× 1.66e-4 4.45e-3 ✓ sig.
regulation of gene expression
GATA6, PDX1, ZNF808
 GO:0010468 3 / 402 23.2× 1.88e-4 4.88e-3 ✓ sig.
cell fate commitment
PTF1A, GATA6
 GO:0045165 2 / 75 83.1× 2.36e-4 5.70e-3 ✓ sig.
liver development
GATA6, PDX1
 GO:0001889 2 / 87 71.6× 3.18e-4 7.04e-3 ✓ sig.
negative regulation of transforming growth factor beta2 production
GATA6
 GO:0032912 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
negative regulation of sebum secreting cell proliferation
GATA6
 GO:1904003 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
cellular response to acadesine
PDX1
 GO:1904102 1 / 1 3,115× 3.21e-4 7.04e-3 ✓ sig.
regulation of DNA-templated transcription
PTF1A, GATA6, PDX1, ZNF808
 GO:0006355 4 / 1,454 8.6× 4.82e-4 9.25e-3 ✓ sig.
regulation of antimicrobial humoral response
GATA6
 GO:0002759 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
response to chlorate
PDX1
 GO:0010157 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.
sebaceous gland cell differentiation
GATA6
 GO:0001949 1 / 2 1,557× 6.42e-4 1.11e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital heart disease with or without pancreatic agenesis or neonatal diabetes Pancreatic agenesis, diaphragmatic hernia, and congenital heart defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Cardiac malformation syndrome Truncus arteriosus 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenital heart disease with or without pancreatic agenesis or neonatal diabetes Truncus arteriosus 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Pancreatic agenesis, diaphragmatic hernia, and congenital heart defects Truncus arteriosus 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Pancreatic beta-cell agenesis with neonatal diabetes mellitus Partial pancreatic agenesis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Congenital heart disease with or without pancreatic agenesis or neonatal diabetes Partial pancreatic agenesis 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Pancreatic agenesis, diaphragmatic hernia, and congenital heart defects Partial pancreatic agenesis 0.200 1 2.58e-4 5.38e-4 ✓ sig.