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 56

15 diseases · 30 shared-gene connections
15 Diseases
37 Unique genes
0.200 Avg. similarity score
Transposition of the great arteries Most-connected disease (9 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 ⇵
Transposition of the great arteries 9 9 11
Discordant ventriculoarterial connection 7 7 4
Congenital camptodactyly 5 5 2
Bowed long bones 4 4 2
Cardiac anomalies - developmental delay - facial dysmorphism syndrome 4 4 1
Developmental delay with facial dysmorphism syndrome 4 4 1
Double outlet right ventricle 4 4 8
Right atrial isomerism 4 4 3
Right isomerism 4 4 1
Buruli ulcer 3 3 2
Congenital hypoplasia of femur 3 3 2
Down syndrome 3 3 19
immunodeficiency 114, folate-responsive 3 3 1
Congenitally uncorrected transposition of the great arteries 2 2 1
asphyxiating thoracic dystrophy 3 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
GDF1 5 / 15 Discordant ventriculoarterial connection, Double outlet right ventricle, Right atrial isomerism, Right isomerism and 1 more
MED13L 5 / 15 Cardiac anomalies - developmental delay - facial dysmorphism syndrome, Congenital camptodactyly, Developmental delay with facial dysmorphism syndrome, Discordant ventriculoarterial connection and 1 more
PLOD2 4 / 15 Bowed long bones, Buruli ulcer, Congenital camptodactyly, Congenital hypoplasia of femur
SLC19A1 4 / 15 Discordant ventriculoarterial connection, Down syndrome, immunodeficiency 114, folate-responsive, Transposition of the great arteries
CERS1 3 / 15 Double outlet right ventricle, Right atrial isomerism, Transposition of the great arteries
CFC1 3 / 15 Congenitally uncorrected transposition of the great arteries, Double outlet right ventricle, Transposition of the great arteries
MTHFR 3 / 15 Discordant ventriculoarterial connection, Down syndrome, Transposition of the great arteries
DYNC2H1 2 / 15 asphyxiating thoracic dystrophy 3, Bowed long bones
UPF1 2 / 15 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 ⇵
Metabolism of folate and pterines
MTHFR, SLC19A1, MTHFD1
 Reactome 3 / 17 57.3× 1.78e-5 5.42e-4 ✓ sig.
Folate transport and metabolism
MTHFR, SLC19A1, MTHFD1
 KEGG 3 / 31 31.4× 1.14e-4 2.49e-3 ✓ sig.
Detoxification of Reactive Oxygen Species
PRDX2, PRDX6, SOD1
 Reactome 3 / 34 28.6× 1.51e-4 3.12e-3 ✓ sig.
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
ISL1, GATA4
 Reactome 2 / 7 92.7× 1.92e-4 3.79e-3 ✓ sig.
Physiological factors
NKX2-5, GATA4
 Reactome 2 / 12 54.1× 5.98e-4 9.16e-3 ✓ sig.
YAP1- and WWTR1 (TAZ)-stimulated gene expression
NKX2-5, GATA4
 Reactome 2 / 14 46.4× 8.21e-4 1.17e-2 ✓ sig.
Factors involved in megakaryocyte development and platelet production
ZFPM2, GATA1, GATA4
 Reactome 3 / 99 9.8× 3.45e-3 3.40e-2 ✓ sig.
Antifolate resistance
MTHFR, SLC19A1
 KEGG 2 / 30 21.6× 3.80e-3 3.64e-2 ✓ sig.
Signaling by SCF-KIT
YES1, MMP9
 Reactome 2 / 37 17.5× 5.75e-3 4.81e-2 ✓ sig.
One carbon pool by folate
MTHFR, MTHFD1
 KEGG 2 / 38 17.1× 6.05e-3 4.96e-2 ✓ sig.
NTF3 activates NTRK3 signaling
NTF3
 Reactome 1 / 2 162× 6.15e-3 5.02e-2
Thyroid hormone signaling pathway
MED13L, RCAN1, GATA4
 KEGG 3 / 122 8.0× 6.18e-3 5.04e-2
Bladder cancer
CXCL8, MMP9
 KEGG 2 / 41 15.8× 7.02e-3 5.47e-2
Toxicity of botulinum toxin type C (BoNT/C)
SNAP25
 Reactome 1 / 3 108× 9.21e-3 6.53e-2
ARL13B-mediated ciliary trafficking of INPP5E
INPP5E
 Reactome 1 / 3 108× 9.21e-3 6.53e-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
DYNC2H1, CFC1, ISL1, NKX2-5, ZFPM2, MTHFD1, GATA4, BMP2
 GO:0007507 8 / 273 14.8× 5.01e-8 6.79e-6 ✓ sig.
cardiac muscle tissue morphogenesis
NKX2-5, ZFPM2, BMP2
 GO:0055008 3 / 13 117× 2.02e-6 1.45e-4 ✓ sig.
atrial septum morphogenesis
ISL1, NKX2-5, GATA4
 GO:0060413 3 / 13 117× 2.02e-6 1.45e-4 ✓ sig.
right ventricular cardiac muscle tissue morphogenesis
NKX2-5, ZFPM2
 GO:0003221 2 / 2 505× 3.81e-6 2.42e-4 ✓ sig.
embryonic heart tube anterior/posterior pattern specification
GATA4, BMP2
 GO:0035054 2 / 3 337× 1.14e-5 5.77e-4 ✓ sig.
astrocyte differentiation
MYCN, S100B, BMP2
 GO:0048708 3 / 25 60.6× 1.59e-5 7.54e-4 ✓ sig.
outflow tract septum morphogenesis
ISL1, NKX2-5, ZFPM2
 GO:0003148 3 / 28 54.1× 2.26e-5 9.89e-4 ✓ sig.
cardiac muscle cell differentiation
NKX2-5, GATA4, BMP2
 GO:0055007 3 / 30 50.5× 2.80e-5 1.16e-3 ✓ sig.
atrioventricular node development
NKX2-5, GATA4
 GO:0003162 2 / 6 168× 5.69e-5 1.98e-3 ✓ sig.
methionine metabolic process
MTHFR, MTHFD1
 GO:0006555 2 / 6 168× 5.69e-5 1.98e-3 ✓ sig.
positive regulation of interleukin-1 alpha production
ISL1, CALCA
 GO:0032730 2 / 7 144× 7.96e-5 2.55e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
SLC11A1, MED13L, ISL1, MYCN, NKX2-5, YES1, ZFPM2, GATA1, GATA4, BMP2
 GO:0045944 10 / 1,208 4.2× 8.56e-5 2.70e-3 ✓ sig.
cell redox homeostasis
SLC11A1, PRDX2, PRDX6
 GO:0045454 3 / 44 34.4× 8.95e-5 2.79e-3 ✓ sig.
cell-cell signaling
CALCA, GATA1, NTF3, GATA4, BMP2
 GO:0007267 5 / 234 10.8× 9.27e-5 2.86e-3 ✓ sig.
embryo implantation
CALCA, MMP9, SOD1
 GO:0007566 3 / 48 31.6× 1.16e-4 3.39e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Discordant ventriculoarterial connection Transposition of the great arteries 0.333 4 1.41e-13 1.91e-12 ✓ sig.
Right atrial isomerism Transposition of the great arteries 0.250 3 2.71e-10 2.74e-9 ✓ sig.
Double outlet right ventricle Transposition of the great arteries 0.176 3 1.52e-8 1.26e-7 ✓ sig.
Double outlet right ventricle Right atrial isomerism 0.200 2 7.08e-7 4.51e-6 ✓ sig.
Discordant ventriculoarterial connection Down syndrome 0.091 2 8.64e-6 4.55e-5 ✓ sig.
Cardiac anomalies - developmental delay - facial dysmorphism syndrome Developmental delay with facial dysmorphism syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Down syndrome Transposition of the great arteries 0.069 2 7.88e-5 2.83e-4 ✓ sig.
Cardiac anomalies - developmental delay - facial dysmorphism syndrome Congenital camptodactyly 0.333 1 1.30e-4 3.90e-4 ✓ sig.
asphyxiating thoracic dystrophy 3 Bowed long bones 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital camptodactyly Developmental delay with facial dysmorphism syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Right atrial isomerism Right isomerism 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Bowed long bones Buruli ulcer 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Congenital camptodactyly Congenital hypoplasia of femur 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Buruli ulcer Congenital hypoplasia of femur 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Buruli ulcer Congenital camptodactyly 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Bowed long bones Congenital hypoplasia of femur 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Bowed long bones Congenital camptodactyly 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Developmental delay with facial dysmorphism syndrome Discordant ventriculoarterial connection 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Discordant ventriculoarterial connection Right isomerism 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Discordant ventriculoarterial connection immunodeficiency 114, folate-responsive 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cardiac anomalies - developmental delay - facial dysmorphism syndrome Discordant ventriculoarterial connection 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Congenitally uncorrected transposition of the great arteries Double outlet right ventricle 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Double outlet right ventricle Right isomerism 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Right isomerism Transposition of the great arteries 0.083 1 7.14e-4 1.31e-3 ✓ sig.
immunodeficiency 114, folate-responsive Transposition of the great arteries 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Developmental delay with facial dysmorphism syndrome Transposition of the great arteries 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Congenitally uncorrected transposition of the great arteries Transposition of the great arteries 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Cardiac anomalies - developmental delay - facial dysmorphism syndrome Transposition of the great arteries 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Discordant ventriculoarterial connection Right atrial isomerism 0.143 1 7.79e-4 1.39e-3 ✓ sig.
Down syndrome immunodeficiency 114, folate-responsive 0.050 1 1.23e-3 1.97e-3 ✓ sig.