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 74

13 diseases · 20 shared-gene connections
13 Diseases
29 Unique genes
0.215 Avg. similarity score
Congenital hypoplasia of aortic arch Most-connected disease (6 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 hypoplasia of aortic arch 6 6 1
Periportal fibrosis 6 6 1
Caroli disease 5 5 4
Urogenital abnormalities 4 4 9
autosomal recessive polycystic kidney disease 4 4 3
Anhydramnios 3 3 11
Cystathionine beta-synthase deficiency 3 3 2
Ventricular hypertrophy 3 3 3
autosomal dominant polycystic kidney disease 2 2 7
Biliary-renal-neuro-skeletal syndrome 1 1 1
radioulnar synostosis with amegakaryocytic thrombocytopenia 1 1 1 1
renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss 1 1 1
renal-hepatic-pancreatic dysplasia 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PKHD1 8 / 13 Anhydramnios, autosomal recessive polycystic kidney disease, Caroli disease, Congenital hypoplasia of aortic arch and 4 more
PKD1 4 / 13 Anhydramnios, autosomal dominant polycystic kidney disease, autosomal recessive polycystic kidney disease, Caroli disease
ATP6V1B1 2 / 13 renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss, Urogenital abnormalities
DNAJB11 2 / 13 Anhydramnios, autosomal dominant polycystic kidney disease
HOXA11 2 / 13 radioulnar synostosis with amegakaryocytic thrombocytopenia 1, Urogenital abnormalities
IFT56 2 / 13 Biliary-renal-neuro-skeletal syndrome, Caroli disease
NEK8 2 / 13 autosomal dominant polycystic kidney disease, renal-hepatic-pancreatic dysplasia 2
PKD2 2 / 13 Anhydramnios, autosomal dominant polycystic kidney disease
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 ⇵
Renin-angiotensin system
ACE, AGT, AGTR1
 KEGG 3 / 23 54.0× 2.17e-5 6.39e-4 ✓ sig.
Hypertrophic cardiomyopathy
ACE, AGT, TGFB2, RYR2
 KEGG 4 / 99 16.7× 8.81e-5 2.02e-3 ✓ sig.
Diabetic cardiomyopathy
ACE, AGT, AGTR1, TGFB2, RYR2
 KEGG 5 / 205 10.1× 1.17e-4 2.55e-3 ✓ sig.
Renin secretion
ACE, AGT, AGTR1
 KEGG 3 / 69 18.0× 5.96e-4 9.14e-3 ✓ sig.
Metabolism of Angiotensinogen to Angiotensins
ACE, AGT
 Reactome 2 / 17 48.7× 7.49e-4 1.09e-2 ✓ sig.
VxPx cargo-targeting to cilium
PKD1, PKD2
 Reactome 2 / 21 39.4× 1.15e-3 1.51e-2 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
AGT, AGTR1, TGFB2
 KEGG 3 / 101 12.3× 1.80e-3 2.11e-2 ✓ sig.
Dilated cardiomyopathy
AGT, TGFB2, RYR2
 KEGG 3 / 105 11.8× 2.01e-3 2.29e-2 ✓ sig.
Peptide ligand-binding receptors
AGT, AGTR1, KISS1R
 Reactome 3 / 106 11.7× 2.07e-3 2.34e-2 ✓ sig.
Defective ALG8 causes ALG8-CDG (CDG-1h)
ALG8
 Reactome 1 / 1 414× 2.41e-3 2.62e-2 ✓ sig.
Vascular smooth muscle contraction
AGT, AGTR1, BRAF
 KEGG 3 / 134 9.3× 4.01e-3 3.78e-2 ✓ sig.
Synthesis of dolichyl-phosphate-glucose
ALG5
 Reactome 1 / 2 207× 4.82e-3 4.28e-2 ✓ sig.
Adrenergic signaling in cardiomyocytes
AGT, AGTR1, RYR2
 KEGG 3 / 154 8.1× 5.92e-3 4.89e-2 ✓ sig.
Cushing syndrome
AGT, AGTR1, BRAF
 KEGG 3 / 155 8.0× 6.02e-3 4.95e-2 ✓ sig.
Cysteine formation from homocysteine
CBS
 Reactome 1 / 3 138× 7.23e-3 5.58e-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 ⇵
kidney development
ACE, AGT, AGTR1, GREB1L, NPHP3, PKD1, PKD2, PKHD1, TGFB2
 GO:0001822 9 / 146 39.7× 7.41e-13 3.49e-10 ✓ sig.
maintenance of blood vessel diameter homeostasis by renin-angiotensin
ACE, AGT, AGTR1
 GO:0002034 3 / 5 387× 3.35e-8 4.82e-6 ✓ sig.
regulation of systemic arterial blood pressure by renin-angiotensin
ACE, AGT, AGTR1
 GO:0003081 3 / 6 322× 6.70e-8 8.67e-6 ✓ sig.
mesonephric duct development
GREB1L, PKD1, PKD2
 GO:0072177 3 / 6 322× 6.70e-8 8.67e-6 ✓ sig.
determination of left/right symmetry
NPHP3, PKD2, NEK8, IFT140, ALG5
 GO:0007368 5 / 83 38.8× 1.67e-7 1.87e-5 ✓ sig.
blood vessel diameter maintenance
ACE, AGT, AGTR1, CBS
 GO:0097746 4 / 37 69.7× 2.98e-7 3.03e-5 ✓ sig.
blood vessel remodeling
ACE, AGT, CBS, TGFB2
 GO:0001974 4 / 42 61.4× 5.03e-7 4.70e-5 ✓ sig.
branching involved in ureteric bud morphogenesis
EYA1, GREB1L, PKD2, HOXA11
 GO:0001658 4 / 45 57.3× 6.67e-7 5.95e-5 ✓ sig.
cilium assembly
NPHP3, PKHD1, TMEM67, WDR19, DZIP1L, IFT140
 GO:0060271 6 / 237 16.3× 1.45e-6 1.12e-4 ✓ sig.
animal organ morphogenesis
EYA1, PKD1, FGD1, BRAF, NEK8
 GO:0009887 5 / 130 24.8× 1.57e-6 1.19e-4 ✓ sig.
angiotensin-activated signaling pathway
ACE, AGT, AGTR1
 GO:0038166 3 / 16 121× 1.86e-6 1.36e-4 ✓ sig.
regulation of renal output by angiotensin
ACE, AGT
 GO:0002019 2 / 2 644× 2.33e-6 1.62e-4 ✓ sig.
regulation of vasoconstriction
ACE, AGT, AGTR1
 GO:0019229 3 / 23 84.0× 5.83e-6 3.39e-4 ✓ sig.
uterus development
GREB1L, HOXA11, TGFB2
 GO:0060065 3 / 23 84.0× 5.83e-6 3.39e-4 ✓ sig.
renin-angiotensin regulation of aldosterone production
AGT, AGTR1
 GO:0002018 2 / 3 430× 6.97e-6 3.91e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Anhydramnios autosomal dominant polycystic kidney disease 0.188 3 9.48e-9 8.05e-8 ✓ sig.
autosomal recessive polycystic kidney disease Caroli disease 0.333 2 1.52e-7 1.09e-6 ✓ sig.
Anhydramnios autosomal recessive polycystic kidney disease 0.154 2 1.39e-6 8.41e-6 ✓ sig.
Anhydramnios Caroli disease 0.143 2 2.78e-6 1.59e-5 ✓ sig.
Congenital hypoplasia of aortic arch Periportal fibrosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital hypoplasia of aortic arch Cystathionine beta-synthase deficiency 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cystathionine beta-synthase deficiency Periportal fibrosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
autosomal recessive polycystic kidney disease Congenital hypoplasia of aortic arch 0.250 1 1.95e-4 5.28e-4 ✓ sig.
autosomal recessive polycystic kidney disease Periportal fibrosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital hypoplasia of aortic arch Ventricular hypertrophy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Periportal fibrosis Ventricular hypertrophy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Biliary-renal-neuro-skeletal syndrome Caroli disease 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Caroli disease Congenital hypoplasia of aortic arch 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Caroli disease Periportal fibrosis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Cystathionine beta-synthase deficiency Ventricular hypertrophy 0.200 1 3.90e-4 8.52e-4 ✓ sig.
autosomal dominant polycystic kidney disease renal-hepatic-pancreatic dysplasia 2 0.125 1 4.55e-4 9.55e-4 ✓ sig.
radioulnar synostosis with amegakaryocytic thrombocytopenia 1 Urogenital abnormalities 0.100 1 5.84e-4 1.14e-3 ✓ sig.
renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss Urogenital abnormalities 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Congenital hypoplasia of aortic arch Urogenital abnormalities 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Periportal fibrosis Urogenital abnormalities 0.100 1 5.84e-4 1.14e-3 ✓ sig.