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 367

5 diseases · 6 shared-gene connections
5 Diseases
72 Unique genes
0.096 Avg. similarity score
Atrial septal defect Most-connected disease (4 links)
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Disease Searched: Atrial 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 ⇵
Atrial septal defect 4 4 35
Congenital heart septal defect 3 3 18
Ventricular septal defect 2 2 42
renpenning syndrome 2 2 1
Bafopathy 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CITED2 3 / 5 Atrial septal defect, Congenital heart septal defect, Ventricular septal defect
GATA4 3 / 5 Atrial septal defect, Congenital heart septal defect, Ventricular septal defect
NKX2-5 3 / 5 Atrial septal defect, Congenital heart septal defect, Ventricular septal defect
PQBP1 3 / 5 Atrial septal defect, Congenital heart septal defect, renpenning syndrome
ACTL6A 2 / 5 Atrial septal defect, Bafopathy
BMP2 2 / 5 Atrial septal defect, Ventricular septal defect
CUL9 2 / 5 Atrial septal defect, Ventricular septal defect
EPO 2 / 5 Congenital heart septal defect, Ventricular septal defect
GATA6 2 / 5 Atrial septal defect, Ventricular septal defect
HSPBAP1 2 / 5 Atrial septal defect, Congenital heart septal defect
HUWE1 2 / 5 Atrial septal defect, Ventricular septal defect
ISL1 2 / 5 Atrial septal defect, Ventricular septal defect
MYH6 2 / 5 Atrial septal defect, Congenital heart septal defect
PARP14 2 / 5 Atrial septal defect, Congenital heart septal defect
PCSK5 2 / 5 Congenital heart septal defect, Ventricular septal defect
ROBO1 2 / 5 Atrial septal defect, Congenital heart septal defect
SALL4 2 / 5 Congenital heart septal defect, Ventricular septal defect
SMARCA4 2 / 5 Atrial septal defect, Ventricular septal defect
TBX20 2 / 5 Atrial septal defect, Ventricular septal defect
TBX5 2 / 5 Atrial septal defect, Ventricular septal defect
YES1 2 / 5 Congenital heart septal defect, Ventricular septal defect
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 ⇵
Molecules associated with elastic fibres
BMP2, TGFB2, BMP4, BMP7, FBN2
 Reactome 5 / 38 21.9× 2.89e-6 1.16e-4 ✓ sig.
Physiological factors
TBX5, GATA4, NKX2-5
 Reactome 3 / 12 41.7× 4.37e-5 1.11e-3 ✓ sig.
Striated Muscle Contraction
TPM1, MYH6, ACTC1, DMD
 Reactome 4 / 36 18.5× 6.05e-5 1.45e-3 ✓ sig.
YAP1- and WWTR1 (TAZ)-stimulated gene expression
TBX5, GATA4, NKX2-5
 Reactome 3 / 14 35.7× 7.17e-5 1.66e-3 ✓ sig.
Proteoglycans in cancer
TGFB2, SOS1, WNT9B, BRAF, COL1A2, FLNA, MMP9
 KEGG 7 / 204 5.7× 2.13e-4 3.99e-3 ✓ sig.
Hypertrophic cardiomyopathy
TGFB2, TPM1, MYH6, ACTC1, DMD
 KEGG 5 / 99 8.4× 3.11e-4 5.41e-3 ✓ sig.
Dilated cardiomyopathy
TGFB2, TPM1, MYH6, ACTC1, DMD
 KEGG 5 / 105 7.9× 4.08e-4 6.74e-3 ✓ sig.
Hepatocellular carcinoma
ACTL6A, TGFB2, SMARCA4, SOS1, WNT9B, BRAF
 KEGG 6 / 170 5.9× 5.31e-4 8.25e-3 ✓ sig.
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
GATA4, ISL1
 Reactome 2 / 7 47.7× 7.30e-4 1.06e-2 ✓ sig.
Signaling by SCF-KIT
SOS1, YES1, MMP9
 Reactome 3 / 37 13.5× 1.39e-3 1.73e-2 ✓ sig.
Regulation of gene expression by Hypoxia-inducible Factor
CITED2, EPO
 Reactome 2 / 11 30.3× 1.88e-3 2.19e-2 ✓ sig.
MAPK signaling pathway
TGFB2, SOS1, BRAF, FLNA, NFATC1, RPS6KA3, TEK
 KEGG 7 / 299 3.9× 2.04e-3 2.31e-2 ✓ sig.
GP1b-IX-V activation signalling
COL1A2, FLNA
 Reactome 2 / 12 27.8× 2.25e-3 2.48e-2 ✓ sig.
Hippo signaling pathway
BMP2, TGFB2, BMP4, WNT9B, BMP7
 KEGG 5 / 157 5.3× 2.48e-3 2.67e-2 ✓ sig.
Cytoskeleton in muscle cells
TPM1, MYH6, ACTC1, DMD, COL1A2, FBN2
 KEGG 6 / 232 4.3× 2.63e-3 2.79e-2 ✓ sig.

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
BMP2, TBX5, TGFB2, GATA4, NKX2-5, CITED2, BMP4, ISL1, PCSK5, SALL4, BMP7, IRX4
 GO:0007507 17 / 273 16.2× 2.52e-16 2.23e-13 ✓ sig.
outflow tract septum morphogenesis
ROBO1, TGFB2, TBX20, NKX2-5, GATA6, BMP4, ISL1, TBX2, TBX1
 GO:0003148 9 / 28 83.4× 7.26e-16 5.87e-13 ✓ sig.
positive regulation of transcription by RNA polymerase II
BMP2, TBX5, GATA4, TBX20, NKX2-5, CITED2, GATA6, BMP4, CHD7, ISL1, SMARCA4, TBX2
 GO:0045944 25 / 1,208 5.4× 1.16e-12 5.20e-10 ✓ sig.
heart morphogenesis
BMP2, TGFB2, NKX2-5, BMP4, CHD7, ISL1, SOS1, TBX2, TBX1
 GO:0003007 9 / 61 38.3× 1.65e-12 7.17e-10 ✓ sig.
endocardial cushion development
TBX5, GATA4, CITED2, BMP4, CRELD1, FOXF1
 GO:0003197 6 / 13 120× 4.44e-12 1.76e-9 ✓ sig.
atrial septum morphogenesis
TBX5, TGFB2, GATA4, TBX20, NKX2-5, ISL1
 GO:0060413 6 / 13 120× 4.44e-12 1.76e-9 ✓ sig.
positive regulation of DNA-templated transcription
ACTL6A, BMP2, TBX5, GATA4, TBX20, NKX2-5, CITED2, GATA6, BMP4, PQBP1, SMARCA4, TBX2
 GO:0045893 20 / 778 6.7× 7.78e-12 2.93e-9 ✓ sig.
regulation of DNA-templated transcription
ACTL6A, BMP2, FOXP1, TBX5, GATA4, TBX20, NKX2-5, CITED2, GATA6, CHD7, ISL1, MN1
 GO:0006355 26 / 1,454 4.6× 9.79e-12 3.61e-9 ✓ sig.
aortic valve morphogenesis
ROBO1, GATA4, TBX20, NKX2-5, BMP4, GATA5, NFATC1
 GO:0003180 7 / 37 49.1× 8.78e-11 2.60e-8 ✓ sig.
outflow tract morphogenesis
TGFB2, TBX20, NKX2-5, CITED2, BMP4, ISL1, TBX2, TBX1
 GO:0003151 8 / 63 33.0× 1.06e-10 3.11e-8 ✓ sig.
pharyngeal system development
NKX2-5, ISL1, TBX2, BMP7, NKX2-6, TBX1
 GO:0060037 6 / 21 74.2× 1.37e-10 3.91e-8 ✓ sig.
skeletal system development
BMP2, TGFB2, TLL1, BMP4, CHD7, BMP7, COL1A2, EVC, MMP9, RPS6KA3
 GO:0001501 10 / 151 17.2× 3.07e-10 7.92e-8 ✓ sig.
atrioventricular canal development
GATA4, TBX20, GATA6, CHD7, TBX2
 GO:0036302 5 / 11 118× 3.35e-10 8.54e-8 ✓ sig.
endocardial cushion formation
ROBO1, BMP2, TBX20, TBX2, BMP7
 GO:0003272 5 / 12 108× 5.72e-10 1.37e-7 ✓ sig.
negative regulation of transcription by RNA polymerase II
BMP2, FOXP1, GATA4, TBX20, NKX2-5, CITED2, GATA6, BMP4, HDAC8, ISL1, SMARCA4, TBX2
 GO:0000122 20 / 1,002 5.2× 6.98e-10 1.63e-7 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Atrial septal defect Ventricular septal defect 0.164 11 5.93e-21 1.18e-19 ✓ sig.
Atrial septal defect Congenital heart septal defect 0.174 8 1.30e-17 2.18e-16 ✓ sig.
Congenital heart septal defect Ventricular septal defect 0.130 7 2.07e-14 2.83e-13 ✓ sig.
Congenital heart septal defect renpenning syndrome 0.053 1 1.17e-3 1.89e-3 ✓ sig.
Atrial septal defect Bafopathy 0.028 1 2.27e-3 3.19e-3 ✓ sig.
Atrial septal defect renpenning syndrome 0.028 1 2.27e-3 3.19e-3 ✓ sig.