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 28

19 diseases · 40 shared-gene connections
19 Diseases
36 Unique genes
0.234 Avg. similarity score
Congenital scoliosis Most-connected disease (10 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 scoliosis 10 10 2
Congenital pectus carinatum 9 9 1
Coronary artery dissection 9 9 1
Geleophysic dysplasia 8 8 3
Crst syndrome 7 7 2
Arthrogryposis-renal dysfunction-cholestasis syndrome 6 6 3
Dilatation of pulmonary artery 5 5 2
Ectopia lentis 5 5 3
Acromesomelic dysplasia 3 3 7
Contracture 3 3 10
Metaphyseal chondrodysplasia 3 3 8
Weill-marchesani syndrome 3 3 4
Dermatosparaxis ehlers-danlos syndrome 2 2 2
Verloes-bourguignon syndrome 2 2 2
Camptodactyly-arthropathy-coxa vara-pericarditis syndrome 1 1 2
Schmid metaphyseal chondrodysplasia 1 1 1
Trident hand 1 1 1
arthrogryposis, renal dysfunction, and cholestasis 1 1 1 1
arthrogryposis, renal dysfunction, and cholestasis 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
FBN1 11 / 19 Acromesomelic dysplasia, Arthrogryposis-renal dysfunction-cholestasis syndrome, Congenital pectus carinatum, Congenital scoliosis and 7 more
LTBP3 4 / 19 Acromesomelic dysplasia, Congenital scoliosis, Geleophysic dysplasia, Verloes-bourguignon syndrome
ADAMTSL2 3 / 19 Contracture, Dermatosparaxis ehlers-danlos syndrome, Geleophysic dysplasia
COL10A1 2 / 19 Metaphyseal chondrodysplasia, Schmid metaphyseal chondrodysplasia
NPR2 2 / 19 Acromesomelic dysplasia, Trident hand
PRG4 2 / 19 Camptodactyly-arthropathy-coxa vara-pericarditis syndrome, Contracture
VIPAS39 2 / 19 arthrogryposis, renal dysfunction, and cholestasis 2, Arthrogryposis-renal dysfunction-cholestasis syndrome
VPS33B 2 / 19 arthrogryposis, renal dysfunction, and cholestasis 1, Arthrogryposis-renal dysfunction-cholestasis syndrome
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 ⇵
Defective B3GALTL causes Peters-plus syndrome (PpS)
ADAMTSL2, ADAMTS2, ADAMTSL4, ADAMTS17, ADAMTS10
 Reactome 5 / 37 45.1× 7.37e-8 5.01e-6 ✓ sig.
O-glycosylation of TSR domain-containing proteins
ADAMTSL2, ADAMTS2, ADAMTSL4, ADAMTS17, ADAMTS10
 Reactome 5 / 38 43.9× 8.47e-8 5.67e-6 ✓ sig.
Molecules associated with elastic fibres
GDF5, FBN1, LTBP3, LTBP2
 Reactome 4 / 38 35.1× 4.67e-6 1.80e-4 ✓ sig.
TGF-beta signaling pathway
BMPR1B, GDF5, FBN1, BMPR2
 KEGG 4 / 108 12.4× 2.92e-4 5.25e-3 ✓ sig.
Hippo signaling pathway
BMPR1B, GDF5, WNT7B, BMPR2
 KEGG 4 / 157 8.5× 1.20e-3 1.55e-2 ✓ sig.
Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate
IDH1
 Reactome 1 / 1 334× 3.00e-3 3.07e-2 ✓ sig.
NADPH regeneration
IDH1
 Reactome 1 / 1 334× 3.00e-3 3.07e-2 ✓ sig.
Signaling by BMP
BMPR1B, BMPR2
 Reactome 2 / 28 23.8× 3.14e-3 3.18e-2 ✓ sig.
Hormone signaling
NPR2, BMPR1B, PRKG2, PTH1R
 KEGG 4 / 219 6.1× 4.01e-3 3.77e-2 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
BMPR1B, WNT7B, BMPR2
 KEGG 3 / 144 7.0× 9.03e-3 6.45e-2
Assembly of collagen fibrils and other multimeric structures
COL10A1, MMP13
 Reactome 2 / 51 13.1× 1.02e-2 6.93e-2
Collagen degradation
COL10A1, MMP13
 Reactome 2 / 52 12.8× 1.05e-2 7.10e-2
cGMP-PKG signaling pathway
NPR2, PRKG2, KCNU1
 KEGG 3 / 166 6.0× 1.33e-2 8.07e-2
Glutathione metabolism
LANCL1, IDH1
 KEGG 2 / 59 11.3× 1.34e-2 8.14e-2
STING mediated induction of host immune responses
DDX41
 Reactome 1 / 5 66.7× 1.49e-2 8.66e-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 ⇵
chondrocyte differentiation
NPR2, BMPR1B, GDF5, LTBP3, PTH1R
 GO:0002062 5 / 61 42.5× 1.09e-7 1.30e-5 ✓ sig.
extracellular matrix organization
ADAMTSL2, ADAMTS2, ADAMTSL4, MMP13, ADAMTS17, ADAMTS10
 GO:0030198 6 / 145 21.5× 3.16e-7 3.18e-5 ✓ sig.
collagen fibril organization
VIPAS39, VPS33B, ANTXR2, ADAMTS2
 GO:0030199 4 / 65 31.9× 7.22e-6 4.03e-4 ✓ sig.
positive regulation of chondrocyte differentiation
BMPR1B, GDF5, PRKG2
 GO:0032332 3 / 20 77.9× 7.32e-6 4.07e-4 ✓ sig.
skeletal system development
FBN1, LTBP3, COL10A1, PTH1R, TRPS1
 GO:0001501 5 / 151 17.2× 9.93e-6 5.19e-4 ✓ sig.
cell surface receptor protein serine/threonine kinase signaling pathway
BMPR1B, GDF5, BMPR2
 GO:0007178 3 / 33 47.2× 3.44e-5 1.36e-3 ✓ sig.
negative regulation of chondrocyte proliferation
BMPR1B, BMPR2
 GO:1902731 2 / 5 208× 3.60e-5 1.41e-3 ✓ sig.
endochondral bone morphogenesis
BMPR1B, BMPR2
 GO:0060350 2 / 6 173× 5.39e-5 1.90e-3 ✓ sig.
lung development
FBN1, WNT7B, ADAMTS2, BMPR2
 GO:0030324 4 / 108 19.2× 5.39e-5 1.90e-3 ✓ sig.
peptidyl-lysine hydroxylation
VIPAS39, VPS33B
 GO:0017185 2 / 7 148× 7.53e-5 2.45e-3 ✓ sig.
bone mineralization
LTBP3, PTH1R, MMP13
 GO:0030282 3 / 56 27.8× 1.70e-4 4.49e-3 ✓ sig.
growth plate cartilage development
NPR2, MMP13
 GO:0003417 2 / 11 94.4× 1.96e-4 4.99e-3 ✓ sig.
phagosome-lysosome fusion
VIPAS39, VPS33B
 GO:0090385 2 / 13 79.9× 2.78e-4 6.35e-3 ✓ sig.
positive regulation of osteoblast differentiation
BMPR1B, WNT7B, BMPR2
 GO:0045669 3 / 78 20.0× 4.52e-4 8.93e-3 ✓ sig.
positive regulation of cartilage development
BMPR1B, BMPR2
 GO:0061036 2 / 17 61.1× 4.82e-4 9.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital scoliosis Geleophysic dysplasia 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Acromesomelic dysplasia Congenital scoliosis 0.250 2 1.77e-7 1.25e-6 ✓ sig.
Acromesomelic dysplasia Geleophysic dysplasia 0.222 2 5.31e-7 3.46e-6 ✓ sig.
Congenital pectus carinatum Coronary artery dissection 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coronary artery dissection Dilatation of pulmonary artery 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Coronary artery dissection Crst syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital scoliosis Coronary artery dissection 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital pectus carinatum Congenital scoliosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital pectus carinatum Crst syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital pectus carinatum Dilatation of pulmonary artery 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Arthrogryposis-renal dysfunction-cholestasis syndrome Coronary artery dissection 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital pectus carinatum Ectopia lentis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Coronary artery dissection Ectopia lentis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital pectus carinatum Geleophysic dysplasia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Coronary artery dissection Geleophysic dysplasia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthrogryposis-renal dysfunction-cholestasis syndrome arthrogryposis, renal dysfunction, and cholestasis 2 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthrogryposis-renal dysfunction-cholestasis syndrome arthrogryposis, renal dysfunction, and cholestasis 1 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthrogryposis-renal dysfunction-cholestasis syndrome Congenital pectus carinatum 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital scoliosis Verloes-bourguignon syndrome 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Congenital scoliosis Dilatation of pulmonary artery 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Crst syndrome Dilatation of pulmonary artery 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Congenital scoliosis Crst syndrome 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Coronary artery dissection Weill-marchesani syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Congenital pectus carinatum Weill-marchesani syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Dermatosparaxis ehlers-danlos syndrome Geleophysic dysplasia 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Geleophysic dysplasia Verloes-bourguignon syndrome 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Crst syndrome Geleophysic dysplasia 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Arthrogryposis-renal dysfunction-cholestasis syndrome Congenital scoliosis 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Dilatation of pulmonary artery Ectopia lentis 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Crst syndrome Ectopia lentis 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Congenital scoliosis Ectopia lentis 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Arthrogryposis-renal dysfunction-cholestasis syndrome Crst syndrome 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Acromesomelic dysplasia Trident hand 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Congenital scoliosis Weill-marchesani syndrome 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Congenital pectus carinatum Metaphyseal chondrodysplasia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Coronary artery dissection Metaphyseal chondrodysplasia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Metaphyseal chondrodysplasia Schmid metaphyseal chondrodysplasia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Camptodactyly-arthropathy-coxa vara-pericarditis syndrome Contracture 0.083 1 1.30e-3 2.04e-3 ✓ sig.
Contracture Dermatosparaxis ehlers-danlos syndrome 0.083 1 1.30e-3 2.04e-3 ✓ sig.
Contracture Geleophysic dysplasia 0.077 1 1.95e-3 2.81e-3 ✓ sig.