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 345

5 diseases · 5 shared-gene connections
5 Diseases
91 Unique genes
0.208 Avg. similarity score
Carpal tunnel syndrome Most-connected disease (3 links)
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Disease Searched: Carpal tunnel syndrome 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 ⇵
Carpal tunnel syndrome 3 3 63
Osteochondrodysplasias 3 3 33
Congenital cartilage disorder 2 2 30
Copper metabolism disorder 1 1 1
Rhizomelic dysplasia, ain-naz type 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ADAMTSL2 3 / 5 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COL10A1 3 / 5 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COL11A1 3 / 5 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COL11A2 3 / 5 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COMP 3 / 5 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
BCL2 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
BMPR1B 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
CCS 2 / 5 Carpal tunnel syndrome, Copper metabolism disorder
CHST3 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
COL2A1 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
COL9A1 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
COL9A2 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
COL9A3 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
DLL3 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
DYM 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
FLNA 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
FLNB 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
FLT1 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
GLB1 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
GNPNAT1 2 / 5 Osteochondrodysplasias, Rhizomelic dysplasia, ain-naz type
HOXA11 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
HSPG2 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
KDR 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
LIFR 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
MATN3 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
PTH1R 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
SLC26A2 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
SOST 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
TGFB1 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
TRPS1 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
TRPV4 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
VEGFA 2 / 5 Congenital cartilage disorder, Osteochondrodysplasias
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 ⇵
ECM proteoglycans
ITGB5, VCAN, COMP, COL2A1, COL9A1, COL9A2, COL9A3, HSPG2, MATN3
 Reactome 9 / 51 23.3× 1.29e-10 1.85e-8 ✓ sig.
Focal adhesion
ITGB5, MYL7, THBS3, COMP, BCL2, COL2A1, COL9A1, COL9A2, COL9A3, FLNA, FLNB, FLT1
 KEGG 14 / 203 9.1× 3.38e-10 4.42e-8 ✓ sig.
Non-integrin membrane-ECM interactions
COL10A1, COL11A1, COL11A2, TTR, COL2A1, HSPG2
 Reactome 6 / 24 33.0× 1.93e-8 1.65e-6 ✓ sig.
Collagen chain trimerization
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3
 Reactome 7 / 44 21.0× 3.46e-8 2.74e-6 ✓ sig.
Collagen biosynthesis and modifying enzymes
ADAMTS14, COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3
 Reactome 8 / 67 15.8× 3.60e-8 2.83e-6 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3
 Reactome 7 / 51 18.1× 1.00e-7 7.03e-6 ✓ sig.
Integrin cell surface interactions
ITGB5, COMP, COL2A1, COL9A1, COL9A2, COL9A3, HSPG2, KDR
 Reactome 8 / 81 13.0× 1.63e-7 1.07e-5 ✓ sig.
Cytoskeleton in muscle cells
COL11A1, COL11A2, FBN2, ITGB5, MYL7, THBS3, VCAN, COMP, COL9A1, COL9A2, COL9A3, HSPG2
 KEGG 12 / 232 6.8× 1.67e-7 1.09e-5 ✓ sig.
ECM-receptor interaction
ITGB5, THBS3, COMP, COL2A1, COL9A1, COL9A2, COL9A3, HSPG2
 KEGG 8 / 89 11.9× 3.40e-7 2.04e-5 ✓ sig.
Signaling by PDGF
THBS3, COL2A1, COL9A1, COL9A2, COL9A3
 Reactome 5 / 33 20.0× 4.49e-6 1.86e-4 ✓ sig.
Molecules associated with elastic fibres
EFEMP1, FBN2, ITGB5, LTBP1, TGFB1
 Reactome 5 / 38 17.4× 9.21e-6 3.33e-4 ✓ sig.
Protein digestion and absorption
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3
 KEGG 7 / 103 9.0× 1.25e-5 4.26e-4 ✓ sig.
NCAM1 interactions
COL2A1, COL9A1, COL9A2, COL9A3
 Reactome 4 / 21 25.1× 1.67e-5 5.44e-4 ✓ sig.
VEGF binds to VEGFR leading to receptor dimerization
FLT1, KDR, VEGFA
 Reactome 3 / 8 49.5× 2.29e-5 7.07e-4 ✓ sig.
PI3K-Akt signaling pathway
ITGB5, THBS3, COMP, BCL2, COL2A1, COL9A1, COL9A2, COL9A3, FLT1, KDR, VEGFA
 KEGG 11 / 361 4.0× 8.54e-5 2.04e-3 ✓ 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 ⇵
skeletal system development
COL10A1, COL11A2, VCAN, COMP, COL2A1, COL9A2, DLL3, HOXA11, MATN3, PTH1R, TRPS1, TRAPPC2
 GO:0001501 12 / 151 16.3× 9.09e-12 3.37e-9 ✓ sig.
cartilage development
COL11A1, COL11A2, COMP, TAPT1, BMPR1B, COL2A1, MATN3
 GO:0051216 7 / 89 16.2× 2.56e-7 2.74e-5 ✓ sig.
chondrocyte differentiation
BMPR1B, COL2A1, HOXA11, PTH1R, SLC26A2, TGFB1
 GO:0002062 6 / 61 20.2× 5.05e-7 4.84e-5 ✓ sig.
collagen fibril organization
ADAMTS14, COL11A1, COL11A2, LOXL1, COMP, COL2A1
 GO:0030199 6 / 65 19.0× 7.40e-7 6.63e-5 ✓ sig.
chondrocyte development
COL11A1, COMP, BMPR1B, HOXA11
 GO:0002063 4 / 21 39.1× 2.96e-6 2.03e-4 ✓ sig.
bone trabecula formation
FBN2, THBS3, VEGFA
 GO:0060346 3 / 8 77.0× 6.15e-6 3.66e-4 ✓ sig.
negative regulation of ossification
SMAD6, BCL2, SOST, TGFB1
 GO:0030279 4 / 27 30.4× 8.48e-6 4.76e-4 ✓ sig.
cartilage development involved in endochondral bone morphogenesis
COL2A1, HOXA11, TRPV4
 GO:0060351 3 / 9 68.5× 9.19e-6 5.07e-4 ✓ sig.
ossification
COMP, TAPT1, BCL2, COL2A1, PTH1R, SOST
 GO:0001503 6 / 110 11.2× 1.61e-5 7.84e-4 ✓ sig.
embryonic liver development
CCDC134, TGFB1
 GO:1990402 2 / 2 205× 2.35e-5 1.04e-3 ✓ sig.
regulation of chondrocyte differentiation
LNPK, HOXA11, TRPS1
 GO:0032330 3 / 12 51.3× 2.38e-5 1.06e-3 ✓ sig.
positive regulation of vascular permeability
TGFB1, TRPV4, VEGFA
 GO:0043117 3 / 12 51.3× 2.38e-5 1.06e-3 ✓ sig.
surfactant homeostasis
KDR, TGFB1, VEGFA
 GO:0043129 3 / 18 34.2× 8.65e-5 2.82e-3 ✓ sig.
smooth muscle cell differentiation
MRTFA, TBX18, WNT4
 GO:0051145 3 / 18 34.2× 8.65e-5 2.82e-3 ✓ sig.
vascular endothelial growth factor signaling pathway
FLT1, KDR, VEGFA
 GO:0038084 3 / 19 32.4× 1.02e-4 3.19e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital cartilage disorder Osteochondrodysplasias 0.882 30 3.54e-90 3.17e-88 ✓ sig.
Carpal tunnel syndrome Congenital cartilage disorder 0.056 5 1.28e-7 8.84e-7 ✓ sig.
Carpal tunnel syndrome Osteochondrodysplasias 0.054 5 2.12e-7 1.41e-6 ✓ sig.
Osteochondrodysplasias Rhizomelic dysplasia, ain-naz type 0.029 1 2.14e-3 3.04e-3 ✓ sig.
Carpal tunnel syndrome Copper metabolism disorder 0.016 1 4.09e-3 5.16e-3 ✓ sig.