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 44

16 diseases · 19 shared-gene connections
16 Diseases
219 Unique genes
0.113 Avg. similarity score
Osteochondrodysplasias Most-connected disease (5 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 ⇵
Osteochondrodysplasias 5 5 33
Spondyloepimetaphyseal dysplasia 5 5 25
Spondyloepiphyseal dysplasia 5 5 18
Congenital cartilage disorder 4 4 30
Connective tissue disease 4 4 117
Carpal tunnel syndrome 3 3 63
B3GALT6-congenital disorder of glycosylation 2 2 1
Mixed connective tissue disease 2 2 24
Cerebrocostomandibular syndrome 1 1 1
Copper metabolism disorder 1 1 1
Hoxha-aliu syndrome 1 1 1
Rhizomelic dysplasia, ain-naz type 1 1 1
schneckenbecken dysplasia 1 1 1
spondyloepimetaphyseal dysplasia with joint laxity, type 3 1 1 1
spondyloepimetaphyseal dysplasia, genevieve type 1 1 1
spondyloepiphyseal dysplasia, kondo-fu type 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL2A1 5 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias, Spondyloepimetaphyseal dysplasia and 1 more
TRPV4 5 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias, Spondyloepimetaphyseal dysplasia and 1 more
COL11A1 4 / 16 Carpal tunnel syndrome, Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL11A2 4 / 16 Carpal tunnel syndrome, Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COMP 4 / 16 Carpal tunnel syndrome, Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
HSPG2 4 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias, Spondyloepiphyseal dysplasia
MATN3 4 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias, Spondyloepimetaphyseal dysplasia
ADAMTSL2 3 / 16 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
B3GALT6 3 / 16 B3GALT6-congenital disorder of glycosylation, Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia
CHST3 3 / 16 Congenital cartilage disorder, Osteochondrodysplasias, Spondyloepiphyseal dysplasia
COL10A1 3 / 16 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COL9A1 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL9A2 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL9A3 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
DYM 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
FLNA 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
FLNB 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
GLB1 3 / 16 Congenital cartilage disorder, Osteochondrodysplasias, Spondyloepiphyseal dysplasia
LIFR 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
PTH1R 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
SLC26A2 3 / 16 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
TRAPPC2 3 / 16 Connective tissue disease, Osteochondrodysplasias, Spondyloepiphyseal dysplasia
ACAN 2 / 16 Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia
BASP1 2 / 16 Connective tissue disease, Mixed connective tissue disease
BCL2 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
BMPR1B 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
CCS 2 / 16 Carpal tunnel syndrome, Copper metabolism disorder
CDH4 2 / 16 Connective tissue disease, Mixed connective tissue disease
CDYL 2 / 16 Connective tissue disease, Mixed connective tissue disease
DDR2 2 / 16 Connective tissue disease, Spondyloepimetaphyseal dysplasia
DLL3 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
EFEMP1 2 / 16 Carpal tunnel syndrome, Connective tissue disease
ERI1 2 / 16 Hoxha-aliu syndrome, Spondyloepimetaphyseal dysplasia
EXOC6B 2 / 16 Spondyloepimetaphyseal dysplasia, spondyloepimetaphyseal dysplasia with joint laxity, type 3
FBN1 2 / 16 Connective tissue disease, Mixed connective tissue disease
FBN2 2 / 16 Carpal tunnel syndrome, Connective tissue disease
FLT1 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
GNPNAT1 2 / 16 Osteochondrodysplasias, Rhizomelic dysplasia, ain-naz type
HDAC4 2 / 16 Connective tissue disease, Mixed connective tissue disease
HHEX 2 / 16 Connective tissue disease, Mixed connective tissue disease
HOXA11 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
KCNMB2 2 / 16 Connective tissue disease, Mixed connective tissue disease
KDR 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
LPAR3 2 / 16 Connective tissue disease, Mixed connective tissue disease
LRP11 2 / 16 Connective tissue disease, Mixed connective tissue disease
MBTPS1 2 / 16 Spondyloepiphyseal dysplasia, spondyloepiphyseal dysplasia, kondo-fu type
MYRIP 2 / 16 Connective tissue disease, Mixed connective tissue disease
NANS 2 / 16 Spondyloepimetaphyseal dysplasia, spondyloepimetaphyseal dysplasia, genevieve type
OFD1 2 / 16 Connective tissue disease, Spondyloepiphyseal dysplasia
PBLD 2 / 16 Connective tissue disease, Mixed connective tissue disease
PCLO 2 / 16 Connective tissue disease, Mixed connective tissue disease
PFKP 2 / 16 Connective tissue disease, Mixed connective tissue disease
PTGIS 2 / 16 Connective tissue disease, Mixed connective tissue disease
PTPRN2 2 / 16 Connective tissue disease, Mixed connective tissue disease
RPL13 2 / 16 Spondyloepimetaphyseal dysplasia, Spondyloepiphyseal dysplasia
SLC35D1 2 / 16 Connective tissue disease, schneckenbecken dysplasia
SLC39A13 2 / 16 Connective tissue disease, Spondyloepimetaphyseal dysplasia
SLC4A10 2 / 16 Connective tissue disease, Mixed connective tissue disease
SNRPB 2 / 16 Cerebrocostomandibular syndrome, Mixed connective tissue disease
SNRPC 2 / 16 Connective tissue disease, Mixed connective tissue disease
SOST 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
SOX14 2 / 16 Connective tissue disease, Mixed connective tissue disease
SPOP 2 / 16 Connective tissue disease, Mixed connective tissue disease
SSX2IP 2 / 16 Connective tissue disease, Mixed connective tissue disease
TGFB1 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
TRIM55 2 / 16 Connective tissue disease, Mixed connective tissue disease
TRPS1 2 / 16 Congenital cartilage disorder, Osteochondrodysplasias
UIMC1 2 / 16 Connective tissue disease, Mixed connective tissue disease
VEGFA 2 / 16 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, COL1A1, COL1A2, COL3A1
 Reactome 16 / 51 17.2× 3.52e-16 1.47e-13 ✓ sig.
Non-integrin membrane-ECM interactions
COL10A1, COL11A1, COL11A2, TTR, COL2A1, HSPG2, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, DDR2
 Reactome 12 / 24 27.4× 2.23e-15 8.05e-13 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 13 / 51 14.0× 4.46e-12 8.54e-10 ✓ sig.
Collagen biosynthesis and modifying enzymes
ADAMTS14, COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1
 Reactome 14 / 67 11.5× 1.24e-11 2.17e-9 ✓ sig.
Collagen chain trimerization
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 12 / 44 15.0× 1.26e-11 2.20e-9 ✓ sig.
Integrin cell surface interactions
ITGB5, COMP, COL2A1, COL9A1, COL9A2, COL9A3, HSPG2, KDR, COL1A1, COL1A2, COL3A1, COL5A1
 Reactome 14 / 81 9.5× 1.84e-10 2.50e-8 ✓ sig.
Cytoskeleton in muscle cells
COL11A1, COL11A2, FBN2, ITGB5, MYL7, THBS3, VCAN, COMP, COL9A1, COL9A2, COL9A3, HSPG2
 KEGG 22 / 232 5.2× 2.32e-10 3.07e-8 ✓ sig.
Collagen degradation
COL10A1, COL11A1, COL11A2, COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, MMP13
 Reactome 10 / 52 10.5× 2.68e-8 2.09e-6 ✓ sig.
MET activates PTK2 signaling
COL11A1, COL11A2, COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 8 / 30 14.6× 4.46e-8 3.22e-6 ✓ sig.
NCAM1 interactions
COL2A1, COL9A1, COL9A2, COL9A3, COL3A1, COL5A1, COL5A2
 Reactome 7 / 21 18.3× 5.70e-8 4.01e-6 ✓ sig.
Signaling by PDGF
THBS3, COL2A1, COL9A1, COL9A2, COL9A3, COL3A1, COL5A1, COL5A2
 Reactome 8 / 33 13.3× 1.01e-7 6.58e-6 ✓ sig.
Extracellular matrix organization
COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 6 / 15 21.9× 1.50e-7 9.29e-6 ✓ sig.
Focal adhesion
ITGB5, MYL7, THBS3, COMP, COL2A1, BCL2, COL9A1, COL9A2, COL9A3, FLNA, FLNB, FLT1
 KEGG 17 / 203 4.6× 1.75e-7 1.06e-5 ✓ sig.
Molecules associated with elastic fibres
EFEMP1, FBN2, ITGB5, LTBP1, TGFB1, BMP7, FBN1, MFAP5
 Reactome 8 / 38 11.5× 3.29e-7 1.86e-5 ✓ sig.
Protein digestion and absorption
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 KEGG 12 / 103 6.4× 3.55e-7 1.99e-5 ✓ 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, BMP7
 GO:0001501 28 / 151 15.8× 9.78e-26 3.32e-22 ✓ sig.
cartilage development
COL11A1, COL11A2, COMP, COL2A1, TAPT1, BMPR1B, MATN3, BMP7, COL3A1, FGFR3, IFT80, SOX9
 GO:0051216 16 / 89 15.3× 6.05e-15 4.07e-12 ✓ sig.
collagen fibril organization
ADAMTS14, COL11A1, COL11A2, LOXL1, COMP, COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, DDR2
 GO:0030199 14 / 65 18.4× 2.19e-14 1.34e-11 ✓ sig.
ossification
COMP, COL2A1, TAPT1, BCL2, PTH1R, SOST, BMP7, COL1A1, DDR2, EIF2AK3, FGFR3, IFT80
 GO:0001503 15 / 110 11.6× 2.94e-12 1.22e-9 ✓ sig.
chondrocyte differentiation
COL2A1, BMPR1B, HOXA11, PTH1R, SLC26A2, TGFB1, COL3A1, FGFR3, IFT80, SOX9, CCN2
 GO:0002062 11 / 61 15.4× 1.11e-10 3.17e-8 ✓ sig.
endochondral ossification
COL2A1, ALPL, CBS, COL1A1, FGFR3, IFT80, PEX7, MMP13
 GO:0001958 8 / 31 22.0× 1.96e-9 4.06e-7 ✓ sig.
cellular response to transforming growth factor beta stimulus
WNT4, TGFB1, ABL1, ACTA2, COL1A1, DDR2, FBN1, SMAD3, SOX9, TGFBR3
 GO:0071560 10 / 67 12.7× 5.51e-9 1.02e-6 ✓ sig.
bone mineralization
COMP, PTH1R, ALPL, COL1A2, EIF2AK3, FGFR3, LOX, SOX9, MMP13
 GO:0030282 9 / 56 13.7× 1.66e-8 2.66e-6 ✓ sig.
bone development
COL2A1, BMPR1B, DYM, HOXA11, SLC10A7, IFT80, TRIP11, WNT1, RPL13, BGN
 GO:0060348 10 / 76 11.2× 1.93e-8 3.03e-6 ✓ sig.
negative regulation of ossification
SMAD6, BCL2, SOST, TGFB1, NOTCH1, SMAD3, SOX9
 GO:0030279 7 / 27 22.1× 2.01e-8 3.13e-6 ✓ sig.
cartilage development involved in endochondral bone morphogenesis
COL2A1, HOXA11, TRPV4, CBS, COL1A1
 GO:0060351 5 / 9 47.4× 2.56e-8 3.85e-6 ✓ sig.
growth plate cartilage development
THBS3, COMP, IFT80, TGFBR2, MMP13
 GO:0003417 5 / 11 38.8× 9.21e-8 1.12e-5 ✓ sig.
cartilage condensation
COL11A1, COL2A1, BMPR1B, SOX9, CCN2, MGP
 GO:0001502 6 / 21 24.4× 1.13e-7 1.34e-5 ✓ sig.
chondrocyte development
COL11A1, COMP, BMPR1B, HOXA11, EIF2AK3, SOX9
 GO:0002063 6 / 21 24.4× 1.13e-7 1.34e-5 ✓ sig.
intraciliary retrograde transport
WDR35, IFT122, IFT43, TTC21B, WDR19
 GO:0035721 5 / 14 30.5× 3.88e-7 3.78e-5 ✓ 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 3.36e-88 ✓ sig.
Connective tissue disease Mixed connective tissue disease 0.183 22 7.99e-46 4.07e-44 ✓ sig.
Connective tissue disease Osteochondrodysplasias 0.127 17 2.95e-28 8.93e-27 ✓ sig.
Congenital cartilage disorder Connective tissue disease 0.121 16 5.67e-27 1.63e-25 ✓ sig.
Osteochondrodysplasias Spondyloepiphyseal dysplasia 0.130 6 1.09e-12 1.39e-11 ✓ sig.
Spondyloepimetaphyseal dysplasia Spondyloepiphyseal dysplasia 0.128 5 6.23e-11 6.69e-10 ✓ sig.
Congenital cartilage disorder Spondyloepiphyseal dysplasia 0.114 5 1.66e-10 1.72e-9 ✓ sig.
Carpal tunnel syndrome Congenital cartilage disorder 0.056 5 1.28e-7 9.34e-7 ✓ sig.
Carpal tunnel syndrome Osteochondrodysplasias 0.054 5 2.12e-7 1.48e-6 ✓ sig.
B3GALT6-congenital disorder of glycosylation Spondyloepiphyseal dysplasia 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Spondyloepiphyseal dysplasia spondyloepiphyseal dysplasia, kondo-fu type 0.053 1 1.17e-3 1.88e-3 ✓ sig.
Cerebrocostomandibular syndrome Mixed connective tissue disease 0.040 1 1.56e-3 2.36e-3 ✓ sig.
B3GALT6-congenital disorder of glycosylation Spondyloepimetaphyseal dysplasia 0.038 1 1.62e-3 2.44e-3 ✓ sig.
Spondyloepimetaphyseal dysplasia spondyloepimetaphyseal dysplasia, genevieve type 0.038 1 1.62e-3 2.44e-3 ✓ sig.
Spondyloepimetaphyseal dysplasia spondyloepimetaphyseal dysplasia with joint laxity, type 3 0.038 1 1.62e-3 2.44e-3 ✓ sig.
Hoxha-aliu syndrome Spondyloepimetaphyseal dysplasia 0.038 1 1.62e-3 2.44e-3 ✓ sig.
Osteochondrodysplasias Rhizomelic dysplasia, ain-naz type 0.029 1 2.14e-3 3.03e-3 ✓ sig.
Carpal tunnel syndrome Copper metabolism disorder 0.016 1 4.09e-3 5.16e-3 ✓ sig.
Connective tissue disease schneckenbecken dysplasia 0.008 1 7.60e-3 8.90e-3 ✓ sig.