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 27

19 diseases · 50 shared-gene connections
19 Diseases
39 Unique genes
0.267 Avg. similarity score
17q23.1q23.2 microdeletion syndrome 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 ⇵
17q23.1q23.2 microdeletion syndrome 10 10 1
Amelia 10 10 1
Chromosome 17q23.1-q23.2 duplication syndrome 10 10 1
Coxopodopatellar syndrome 10 10 1
Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 9 9 1
Clubfoot 7 7 6
Sacral agenesis 7 7 4
Arthropathy 6 6 3
Tetra-amelia syndrome 6 6 4
Congenital hypoplasia of lung 5 5 3
Patellar aplasia 5 5 2
Congenital clubfoot 3 3 23
Vitamin a deficiency 3 3 5
Bmp4-related ocular growth disorder 2 2 1
ehlers-danlos syndrome, musculocontractural type 1 2 2 1
nail-patella syndrome 2 2 1
progressive pseudorheumatoid arthropathy of childhood 1 1 1
progressive retinal dystrophy due to retinol transport defect 1 1 1
tetraamelia syndrome 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
TBX4 11 / 19 17q23.1q23.2 microdeletion syndrome, Amelia, Arthropathy, Chromosome 17q23.1-q23.2 duplication syndrome and 7 more
BMP4 3 / 19 Bmp4-related ocular growth disorder, Sacral agenesis, Vitamin a deficiency
CHST14 3 / 19 Clubfoot, Congenital clubfoot, ehlers-danlos syndrome, musculocontractural type 1
LMX1B 3 / 19 Clubfoot, Congenital clubfoot, nail-patella syndrome
CCN6 2 / 19 Arthropathy, progressive pseudorheumatoid arthropathy of childhood
MTHFR 2 / 19 Clubfoot, Congenital clubfoot
PITX1 2 / 19 Clubfoot, Congenital clubfoot
RBP4 2 / 19 progressive retinal dystrophy due to retinol transport defect, Vitamin a deficiency
RYR1 2 / 19 Congenital clubfoot, Sacral agenesis
WNT3 2 / 19 Tetra-amelia syndrome, tetraamelia syndrome 1
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 ⇵
Cohesin Loading onto Chromatin
WAPL, NIPBL
 Reactome 2 / 10 61.6× 4.55e-4 7.40e-3 ✓ sig.
Retinoid cycle disease events
LRAT, RBP4
 Reactome 2 / 13 47.4× 7.84e-4 1.13e-2 ✓ sig.
Aminoacyl-tRNA biosynthesis
AARS1, DARS2, AARS2
 KEGG 3 / 66 14.0× 1.26e-3 1.61e-2 ✓ sig.
The canonical retinoid cycle in rods (twilight vision)
LRAT, RBP4
 Reactome 2 / 20 30.8× 1.88e-3 2.18e-2 ✓ sig.
Mtb iron assimilation by chelation
LTF
 Reactome 1 / 1 308× 3.25e-3 3.26e-2 ✓ sig.
Retinoid metabolism disease events
RBP4
 Reactome 1 / 1 308× 3.25e-3 3.26e-2 ✓ sig.
Retinoid metabolism and transport
LRAT, RBP4
 Reactome 2 / 41 15.0× 7.78e-3 5.86e-2
ARL13B-mediated ciliary trafficking of INPP5E
INPP5E
 Reactome 1 / 3 103× 9.71e-3 6.74e-2
Biosynthesis of protectins
CYP1A1
 Reactome 1 / 4 77.0× 1.29e-2 7.95e-2
Ion homeostasis
ATP2B1, RYR1
 Reactome 2 / 54 11.4× 1.32e-2 8.07e-2
Hippo signaling pathway
BMP4, BMP5, WNT3
 KEGG 3 / 157 5.9× 1.42e-2 8.43e-2
Lysine degradation
NSD2, PLOD2
 KEGG 2 / 63 9.8× 1.77e-2 9.64e-2
Basal cell carcinoma
BMP4, WNT3
 KEGG 2 / 63 9.8× 1.77e-2 9.64e-2
Metal sequestration by antimicrobial proteins
LTF
 Reactome 1 / 6 51.3× 1.93e-2 1.01e-1
Collagen biosynthesis and modifying enzymes
COL5A1, PLOD2
 Reactome 2 / 67 9.2× 1.99e-2 1.02e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
embryonic hindlimb morphogenesis
TBX4, BMP4, PITX1, WNT3, RSPO2
 GO:0035116 5 / 29 82.6× 3.47e-9 6.74e-7 ✓ sig.
tRNA aminoacylation
AARS1, DARS2, AARS2
 GO:0043039 3 / 13 111× 2.37e-6 1.65e-4 ✓ sig.
heart morphogenesis
BMP4, COL5A1, NIPBL, TBXT
 GO:0003007 4 / 61 31.4× 7.76e-6 4.28e-4 ✓ sig.
alanyl-tRNA aminoacylation
AARS1, AARS2
 GO:0006419 2 / 3 319× 1.27e-5 6.29e-4 ✓ sig.
skeletal system development
BMP4, PITX1, HOXD12, HOXD13, BMP5
 GO:0001501 5 / 151 15.9× 1.49e-5 7.13e-4 ✓ sig.
heart development
BMP4, CC2D2A, PKD1, NIPBL, BMP5, RBP4
 GO:0007507 6 / 273 10.5× 2.00e-5 8.99e-4 ✓ sig.
eye morphogenesis
COL5A1, NIPBL
 GO:0048592 2 / 4 240× 2.54e-5 1.08e-3 ✓ sig.
response to hypoxia
MTHFR, CYP1A1, PLOD2, RYR1, TRPV4
 GO:0001666 5 / 176 13.6× 3.11e-5 1.25e-3 ✓ sig.
cartilage development
BMP4, PITX1, PKD1, BMP5
 GO:0051216 4 / 89 21.5× 3.48e-5 1.37e-3 ✓ sig.
regulation of branching involved in prostate gland morphogenesis
BMP4, HOXD13
 GO:0060687 2 / 5 192× 4.23e-5 1.59e-3 ✓ sig.
embryonic forelimb morphogenesis
NIPBL, WNT3, RSPO2
 GO:0035115 3 / 33 43.6× 4.39e-5 1.64e-3 ✓ sig.
digestive tract development
CYP1A1, PKD1, NIPBL
 GO:0048565 3 / 34 42.3× 4.81e-5 1.74e-3 ✓ sig.
mesoderm formation
BMP4, TBXT, WNT3
 GO:0001707 3 / 38 37.8× 6.74e-5 2.25e-3 ✓ sig.
embryonic organ morphogenesis
NIPBL, RBP4
 GO:0048562 2 / 7 137× 8.85e-5 2.76e-3 ✓ sig.
positive regulation of SMAD protein signal transduction
BMP4, BMP5, PARP1
 GO:0060391 3 / 42 34.2× 9.12e-5 2.83e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Clubfoot Congenital clubfoot 0.154 4 5.66e-11 6.13e-10 ✓ sig.
17q23.1q23.2 microdeletion syndrome Chromosome 17q23.1-q23.2 duplication syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Coxopodopatellar syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 0.500 1 6.49e-5 2.34e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Amelia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Amelia Chromosome 17q23.1-q23.2 duplication syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Amelia Coxopodopatellar syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Amelia Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Coxopodopatellar syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxopodopatellar syndrome Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxopodopatellar syndrome Patellar aplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Patellar aplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension Patellar aplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Amelia Patellar aplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Patellar aplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital hypoplasia of lung Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital hypoplasia of lung Coxopodopatellar syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Congenital hypoplasia of lung 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Amelia Congenital hypoplasia of lung 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthropathy progressive pseudorheumatoid arthropathy of childhood 0.250 1 1.95e-4 5.28e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Congenital hypoplasia of lung 0.250 1 1.95e-4 5.28e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Arthropathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthropathy Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthropathy Coxopodopatellar syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Arthropathy Chromosome 17q23.1-q23.2 duplication syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Amelia Arthropathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Amelia Tetra-amelia syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Coxopodopatellar syndrome Sacral agenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Sacral agenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Amelia Sacral agenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Sacral agenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension Sacral agenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Tetra-amelia syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Tetra-amelia syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Bmp4-related ocular growth disorder Sacral agenesis 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Coxopodopatellar syndrome Tetra-amelia syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Ischiocoxopodopatellar syndrome with pulmonary arterial hypertension Tetra-amelia syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Tetra-amelia syndrome tetraamelia syndrome 1 0.200 1 2.60e-4 6.40e-4 ✓ sig.
progressive retinal dystrophy due to retinol transport defect Vitamin a deficiency 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Bmp4-related ocular growth disorder Vitamin a deficiency 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Clubfoot Coxopodopatellar syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Clubfoot nail-patella syndrome 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Clubfoot ehlers-danlos syndrome, musculocontractural type 1 0.143 1 3.90e-4 8.52e-4 ✓ sig.
17q23.1q23.2 microdeletion syndrome Clubfoot 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Amelia Clubfoot 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Chromosome 17q23.1-q23.2 duplication syndrome Clubfoot 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Sacral agenesis Vitamin a deficiency 0.111 1 1.30e-3 2.04e-3 ✓ sig.
Congenital clubfoot nail-patella syndrome 0.042 1 1.49e-3 2.29e-3 ✓ sig.
Congenital clubfoot ehlers-danlos syndrome, musculocontractural type 1 0.042 1 1.49e-3 2.29e-3 ✓ sig.