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 133

9 diseases · 10 shared-gene connections
9 Diseases
191 Unique genes
0.152 Avg. similarity score
Connective tissue disease Most-connected disease (4 links)
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Disease Searched: schneckenbecken dysplasia 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 ⇵
Connective tissue disease 4 4 117
Osteochondrodysplasias 4 4 33
Carpal tunnel syndrome 3 3 63
Congenital cartilage disorder 3 3 30
Mixed connective tissue disease 2 2 24
Cerebrocostomandibular syndrome 1 1 1
Copper metabolism disorder 1 1 1
Rhizomelic dysplasia, ain-naz type 1 1 1
schneckenbecken dysplasia 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL11A1 4 / 9 Carpal tunnel syndrome, Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL11A2 4 / 9 Carpal tunnel syndrome, Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COMP 4 / 9 Carpal tunnel syndrome, Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
ADAMTSL2 3 / 9 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COL10A1 3 / 9 Carpal tunnel syndrome, Congenital cartilage disorder, Osteochondrodysplasias
COL2A1 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL9A1 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL9A2 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
COL9A3 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
DYM 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
FLNA 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
FLNB 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
HSPG2 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
LIFR 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
MATN3 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
PTH1R 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
SLC26A2 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
TRPV4 3 / 9 Congenital cartilage disorder, Connective tissue disease, Osteochondrodysplasias
BASP1 2 / 9 Connective tissue disease, Mixed connective tissue disease
BCL2 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
BMPR1B 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
CCS 2 / 9 Carpal tunnel syndrome, Copper metabolism disorder
CDH4 2 / 9 Connective tissue disease, Mixed connective tissue disease
CDYL 2 / 9 Connective tissue disease, Mixed connective tissue disease
CHST3 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
DLL3 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
EFEMP1 2 / 9 Carpal tunnel syndrome, Connective tissue disease
FBN1 2 / 9 Connective tissue disease, Mixed connective tissue disease
FBN2 2 / 9 Carpal tunnel syndrome, Connective tissue disease
FLT1 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
GLB1 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
GNPNAT1 2 / 9 Osteochondrodysplasias, Rhizomelic dysplasia, ain-naz type
HDAC4 2 / 9 Connective tissue disease, Mixed connective tissue disease
HHEX 2 / 9 Connective tissue disease, Mixed connective tissue disease
HOXA11 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
KCNMB2 2 / 9 Connective tissue disease, Mixed connective tissue disease
KDR 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
LPAR3 2 / 9 Connective tissue disease, Mixed connective tissue disease
LRP11 2 / 9 Connective tissue disease, Mixed connective tissue disease
MYRIP 2 / 9 Connective tissue disease, Mixed connective tissue disease
PBLD 2 / 9 Connective tissue disease, Mixed connective tissue disease
PCLO 2 / 9 Connective tissue disease, Mixed connective tissue disease
PFKP 2 / 9 Connective tissue disease, Mixed connective tissue disease
PTGIS 2 / 9 Connective tissue disease, Mixed connective tissue disease
PTPRN2 2 / 9 Connective tissue disease, Mixed connective tissue disease
SLC35D1 2 / 9 Connective tissue disease, schneckenbecken dysplasia
SLC4A10 2 / 9 Connective tissue disease, Mixed connective tissue disease
SNRPB 2 / 9 Cerebrocostomandibular syndrome, Mixed connective tissue disease
SNRPC 2 / 9 Connective tissue disease, Mixed connective tissue disease
SOST 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
SOX14 2 / 9 Connective tissue disease, Mixed connective tissue disease
SPOP 2 / 9 Connective tissue disease, Mixed connective tissue disease
SSX2IP 2 / 9 Connective tissue disease, Mixed connective tissue disease
TGFB1 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
TRAPPC2 2 / 9 Connective tissue disease, Osteochondrodysplasias
TRIM55 2 / 9 Connective tissue disease, Mixed connective tissue disease
TRPS1 2 / 9 Congenital cartilage disorder, Osteochondrodysplasias
UIMC1 2 / 9 Connective tissue disease, Mixed connective tissue disease
VEGFA 2 / 9 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 ⇵
Non-integrin membrane-ECM interactions
COL10A1, COL11A1, COL11A2, TTR, COL2A1, HSPG2, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, DDR2
 Reactome 12 / 24 31.4× 4.24e-16 1.56e-13 ✓ sig.
ECM proteoglycans
ITGB5, VCAN, COMP, COL2A1, COL9A1, COL9A2, COL9A3, HSPG2, MATN3, COL1A1, COL1A2, COL3A1
 Reactome 14 / 51 17.3× 3.17e-14 8.18e-12 ✓ sig.
Collagen biosynthesis and modifying enzymes
ADAMTS14, COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1
 Reactome 14 / 67 13.1× 1.92e-12 3.65e-10 ✓ sig.
Collagen chain trimerization
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 12 / 44 17.1× 2.50e-12 4.66e-10 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 12 / 51 14.8× 1.71e-11 2.73e-9 ✓ sig.
Integrin cell surface interactions
ITGB5, COMP, COL2A1, COL9A1, COL9A2, COL9A3, HSPG2, KDR, COL1A1, COL1A2, COL3A1, COL5A1
 Reactome 14 / 81 10.9× 2.95e-11 4.47e-9 ✓ sig.
Cytoskeleton in muscle cells
COL11A1, COL11A2, FBN2, ITGB5, MYL7, THBS3, VCAN, COMP, COL9A1, COL9A2, COL9A3, HSPG2
 KEGG 21 / 232 5.7× 1.12e-10 1.52e-8 ✓ sig.
MET activates PTK2 signaling
COL11A1, COL11A2, COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 8 / 30 16.8× 1.53e-8 1.20e-6 ✓ sig.
NCAM1 interactions
COL2A1, COL9A1, COL9A2, COL9A3, COL3A1, COL5A1, COL5A2
 Reactome 7 / 21 21.0× 2.22e-8 1.66e-6 ✓ sig.
Focal adhesion
ITGB5, MYL7, THBS3, COMP, BCL2, COL2A1, COL9A1, COL9A2, COL9A3, FLNA, FLNB, FLT1
 KEGG 17 / 203 5.3× 2.35e-8 1.75e-6 ✓ sig.
Signaling by PDGF
THBS3, COL2A1, COL9A1, COL9A2, COL9A3, COL3A1, COL5A1, COL5A2
 Reactome 8 / 33 15.2× 3.49e-8 2.50e-6 ✓ sig.
Extracellular matrix organization
COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 6 / 15 25.2× 6.65e-8 4.44e-6 ✓ sig.
Protein digestion and absorption
COL10A1, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 KEGG 12 / 103 7.3× 8.01e-8 5.22e-6 ✓ sig.
Collagen degradation
COL10A1, COL11A1, COL11A2, COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2
 Reactome 9 / 52 10.9× 1.10e-7 6.87e-6 ✓ sig.
Molecules associated with elastic fibres
EFEMP1, FBN2, ITGB5, LTBP1, TGFB1, BMP7, FBN1, MFAP5
 Reactome 8 / 38 13.2× 1.15e-7 7.13e-6 ✓ 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 27 / 151 17.5× 4.88e-26 1.91e-22 ✓ sig.
collagen fibril organization
ADAMTS14, COL11A1, COL11A2, LOXL1, COMP, COL2A1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, DDR2
 GO:0030199 14 / 65 21.1× 3.25e-15 2.30e-12 ✓ sig.
cartilage development
COL11A1, COL11A2, COMP, TAPT1, BMPR1B, COL2A1, MATN3, BMP7, COL3A1, FGFR3, IFT80, SOX9
 GO:0051216 14 / 89 15.4× 3.28e-13 1.63e-10 ✓ sig.
ossification
COMP, TAPT1, BCL2, COL2A1, PTH1R, SOST, BMP7, COL1A1, DDR2, EIF2AK3, FGFR3, IFT80
 GO:0001503 13 / 110 11.6× 9.84e-11 2.90e-8 ✓ sig.
chondrocyte differentiation
BMPR1B, COL2A1, HOXA11, PTH1R, SLC26A2, TGFB1, COL3A1, FGFR3, IFT80, SOX9
 GO:0002062 10 / 61 16.0× 5.64e-10 1.36e-7 ✓ sig.
cellular response to transforming growth factor beta stimulus
WNT4, TGFB1, ABL1, ACTA2, COL1A1, DDR2, FBN1, SMAD3, SOX9, TGFBR3
 GO:0071560 10 / 67 14.6× 1.47e-9 3.15e-7 ✓ sig.
negative regulation of ossification
SMAD6, BCL2, SOST, TGFB1, NOTCH1, SMAD3, SOX9
 GO:0030279 7 / 27 25.4× 7.80e-9 1.36e-6 ✓ sig.
cartilage development involved in endochondral bone morphogenesis
COL2A1, HOXA11, TRPV4, CBS, COL1A1
 GO:0060351 5 / 9 54.4× 1.29e-8 2.11e-6 ✓ sig.
endochondral ossification
COL2A1, ALPL, CBS, COL1A1, FGFR3, IFT80, PEX7
 GO:0001958 7 / 31 22.1× 2.23e-8 3.38e-6 ✓ sig.
chondrocyte development
COL11A1, COMP, BMPR1B, HOXA11, EIF2AK3, SOX9
 GO:0002063 6 / 21 28.0× 5.03e-8 6.75e-6 ✓ sig.
bone mineralization
COMP, PTH1R, ALPL, COL1A2, EIF2AK3, FGFR3, LOX, SOX9
 GO:0030282 8 / 56 14.0× 9.60e-8 1.16e-5 ✓ sig.
intraciliary retrograde transport
WDR35, IFT122, IFT43, TTC21B, WDR19
 GO:0035721 5 / 14 34.9× 1.97e-7 2.13e-5 ✓ sig.
bone trabecula formation
FBN2, THBS3, VEGFA, COL1A1
 GO:0060346 4 / 8 48.9× 7.17e-7 6.30e-5 ✓ sig.
bone development
BMPR1B, COL2A1, DYM, HOXA11, SLC10A7, IFT80, TRIP11, WNT1
 GO:0060348 8 / 76 10.3× 1.07e-6 8.79e-5 ✓ sig.
epithelial to mesenchymal transition
WNT4, TGFB1, BMP7, NOTCH1, SOX9, TGFBR2, TGFBR3
 GO:0001837 7 / 61 11.2× 2.86e-6 1.92e-4 ✓ 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 3.18e-88 ✓ sig.
Connective tissue disease Mixed connective tissue disease 0.183 22 7.99e-46 3.84e-44 ✓ sig.
Connective tissue disease Osteochondrodysplasias 0.127 17 2.95e-28 8.44e-27 ✓ sig.
Congenital cartilage disorder Connective tissue disease 0.121 16 5.67e-27 1.54e-25 ✓ 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.
Cerebrocostomandibular syndrome Mixed connective tissue disease 0.040 1 1.56e-3 2.38e-3 ✓ 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.
Connective tissue disease schneckenbecken dysplasia 0.008 1 7.60e-3 8.89e-3 ✓ sig.