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 520

5 diseases · 8 shared-gene connections
5 Diseases
17 Unique genes
0.153 Avg. similarity score
Double outlet right ventricle Most-connected disease (4 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 ⇵
Double outlet right ventricle 4 4 8
Transposition of the great arteries 4 4 12
Right atrial isomerism 3 3 3
Right isomerism 3 3 1
Congenitally uncorrected transposition of the great arteries 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GDF1 4 / 5 Double outlet right ventricle, Right atrial isomerism, Right isomerism, Transposition of the great arteries
CERS1 3 / 5 Double outlet right ventricle, Right atrial isomerism, Transposition of the great arteries
CFC1 3 / 5 Congenitally uncorrected transposition of the great arteries, Double outlet right ventricle, Transposition of the great arteries
UPF1 2 / 5 Right atrial isomerism, Transposition of the great arteries
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 ⇵
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
ISL1, GATA4
 Reactome 2 / 7 202× 3.94e-5 9.05e-4 ✓ sig.
Physiological factors
NKX2-5, GATA4
 Reactome 2 / 12 118× 1.23e-4 2.24e-3 ✓ sig.
YAP1- and WWTR1 (TAZ)-stimulated gene expression
NKX2-5, GATA4
 Reactome 2 / 14 101× 1.70e-4 2.89e-3 ✓ sig.
Metabolism of folate and pterines
MTHFR, SLC19A1
 Reactome 2 / 17 83.1× 2.53e-4 3.95e-3 ✓ sig.
Antifolate resistance
MTHFR, SLC19A1
 KEGG 2 / 30 47.1× 8.01e-4 9.57e-3 ✓ sig.
Folate transport and metabolism
MTHFR, SLC19A1
 KEGG 2 / 31 45.6× 8.56e-4 1.01e-2 ✓ sig.
Cytokine-cytokine receptor interaction
GDF1, ACVR1B, BMP2
 KEGG 3 / 298 7.1× 7.94e-3 4.94e-2 ✓ sig.
Factors involved in megakaryocyte development and platelet production
ZFPM2, GATA4
 Reactome 2 / 99 14.3× 8.44e-3 5.12e-2
TGF-beta signaling pathway
ACVR1B, BMP2
 KEGG 2 / 108 13.1× 9.98e-3 5.67e-2
Thyroid hormone signaling pathway
GATA4, MED13L
 KEGG 2 / 122 11.6× 1.26e-2 6.55e-2
CD28 co-stimulation
YES1
 Reactome 1 / 9 78.5× 1.27e-2 6.57e-2
Signaling by Activin
ACVR1B
 Reactome 1 / 11 64.2× 1.55e-2 7.39e-2
Transcriptional regulation by RUNX2
BMP2
 Reactome 1 / 12 58.9× 1.69e-2 7.78e-2
FCGR activation
YES1
 Reactome 1 / 12 58.9× 1.69e-2 7.78e-2
PECAM1 interactions
YES1
 Reactome 1 / 12 58.9× 1.69e-2 7.78e-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 ⇵
heart development
CFC1, ISL1, NKX2-5, ZFPM2, GATA4, BMP2
 GO:0007507 6 / 273 24.2× 9.95e-8 1.26e-5 ✓ sig.
cardiac muscle tissue morphogenesis
NKX2-5, ZFPM2, BMP2
 GO:0055008 3 / 13 254× 1.78e-7 2.05e-5 ✓ sig.
atrial septum morphogenesis
ISL1, NKX2-5, GATA4
 GO:0060413 3 / 13 254× 1.78e-7 2.05e-5 ✓ sig.
right ventricular cardiac muscle tissue morphogenesis
NKX2-5, ZFPM2
 GO:0003221 2 / 2 1,099× 7.79e-7 6.99e-5 ✓ sig.
outflow tract septum morphogenesis
ISL1, NKX2-5, ZFPM2
 GO:0003148 3 / 28 118× 2.02e-6 1.53e-4 ✓ sig.
embryonic heart tube anterior/posterior pattern specification
GATA4, BMP2
 GO:0035054 2 / 3 733× 2.34e-6 1.72e-4 ✓ sig.
cardiac muscle cell differentiation
NKX2-5, GATA4, BMP2
 GO:0055007 3 / 30 110× 2.50e-6 1.82e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
ISL1, MYCN, NKX2-5, YES1, ZFPM2, GATA4, MED13L, BMP2
 GO:0045944 8 / 1,208 7.3× 4.28e-6 2.80e-4 ✓ sig.
atrioventricular node development
NKX2-5, GATA4
 GO:0003162 2 / 6 366× 1.17e-5 6.12e-4 ✓ sig.
cell differentiation
ISL1, NKX2-5, YES1, ZFPM2, GATA4, BMP2, CFAP53
 GO:0030154 7 / 1,051 7.3× 2.06e-5 9.46e-4 ✓ sig.
heart morphogenesis
ISL1, NKX2-5, BMP2
 GO:0003007 3 / 61 54.1× 2.18e-5 9.86e-4 ✓ sig.
outflow tract morphogenesis
ISL1, NKX2-5, ZFPM2
 GO:0003151 3 / 63 52.3× 2.40e-5 1.06e-3 ✓ sig.
cardiac ventricle morphogenesis
NKX2-5, GATA4
 GO:0003208 2 / 10 220× 3.49e-5 1.41e-3 ✓ sig.
mesenchymal cell differentiation
ISL1, BMP2
 GO:0048762 2 / 13 169× 6.04e-5 2.13e-3 ✓ sig.
cardiac right ventricle morphogenesis
ISL1, GATA4
 GO:0003215 2 / 13 169× 6.04e-5 2.13e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Right atrial isomerism Transposition of the great arteries 0.231 3 3.55e-10 3.18e-9 ✓ sig.
Double outlet right ventricle Transposition of the great arteries 0.167 3 1.99e-8 1.53e-7 ✓ sig.
Double outlet right ventricle Right atrial isomerism 0.200 2 7.00e-7 4.35e-6 ✓ sig.
Right atrial isomerism Right isomerism 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Congenitally uncorrected transposition of the great arteries Double outlet right ventricle 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Double outlet right ventricle Right isomerism 0.111 1 5.17e-4 9.13e-4 ✓ sig.
Congenitally uncorrected transposition of the great arteries Transposition of the great arteries 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Right isomerism Transposition of the great arteries 0.077 1 7.75e-4 1.25e-3 ✓ sig.