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 112

12 diseases · 19 shared-gene connections
12 Diseases
99 Unique genes
0.162 Avg. similarity score
Skeletal dysplasia Most-connected disease (8 links)
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Disease Searched: Joint laxity, short stature, and myopia 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 ⇵
Skeletal dysplasia 8 8 42
Larsen syndrome 6 6 17
Bone fragility with contractures, arterial rupture, and deafness 5 5 49
Osteoporosis-pseudoglioma syndrome 5 5 49
Osteogenesis imperfecta 4 4 41
Cole-carpenter syndrome 3 3 3
Skeletal dysplasia, mild, with joint laxity and advanced bone age 2 2 1
Craniotubular dysplasia 1 1 1
Dysostosis multiplex, ain-naz type 1 1 1
Immunoskeletal dysplasia with neurodevelopmental abnormalities 1 1 1
Joint laxity, short stature, and myopia 1 1 1
Spondyloepimetaphyseal dysplasia with joint laxity, 2 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
B4GALT7 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
CHST3 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
COL1A1 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
COL1A2 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
CRTAP 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
GORAB 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
P4HB 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
PLOD2 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
SEC24D 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
SERPINH1 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
XYLT2 4 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
ALPL 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
B3GALT6 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
B3GAT3 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
BMP1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
CCDC134 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
CREB3L1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
CSGALNACT1 3 / 12 Larsen syndrome, Skeletal dysplasia, Skeletal dysplasia, mild, with joint laxity and advanced bone age
FKBP10 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
IFITM5 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
KDELR2 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
KIF5B 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
LRP5 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
MBTPS2 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
MESD 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
P3H1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
P4HA1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
PHLDB1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
PLOD3 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
PLS3 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
PPIB 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
SERPINF1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
SLC10A7 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome, Skeletal dysplasia
SP7 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
SPARC 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
TAPT1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
TENT5A 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
TMEM38B 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
WNT1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
XYLT1 3 / 12 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
AMBN 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
COPB2 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
DSPP 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
EMILIN1 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
EXTL3 2 / 12 Immunoskeletal dysplasia with neurodevelopmental abnormalities, Skeletal dysplasia
FGFR3 2 / 12 Larsen syndrome, Skeletal dysplasia
GZF1 2 / 12 Joint laxity, short stature, and myopia, Larsen syndrome
KIF22 2 / 12 Larsen syndrome, Spondyloepimetaphyseal dysplasia with joint laxity, 2
LIFR 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
LYSET 2 / 12 Dysostosis multiplex, ain-naz type, Skeletal dysplasia
MIA3 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
NBAS 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
SEC16B 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
SGMS2 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
SUCO 2 / 12 Osteogenesis imperfecta, Skeletal dysplasia
TMEM53 2 / 12 Craniotubular dysplasia, Skeletal dysplasia
WNT11 2 / 12 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma 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 ⇵
Collagen biosynthesis and modifying enzymes
BMP1, COL1A1, COL1A2, CRTAP, P3H1, P4HA1, P4HB, PLOD2, PLOD3, PPIB, SERPINH1, COL11A1
 Reactome 14 / 67 25.3× 1.77e-16 6.57e-14 ✓ sig.
Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate
B3GALT6, B3GAT3, B4GALT7, CHST3, XYLT1, XYLT2, CSGALNACT1
 KEGG 7 / 21 40.4× 2.21e-10 2.24e-8 ✓ sig.
Glycosaminoglycan biosynthesis - heparan sulfate / heparin
B3GALT6, B3GAT3, B4GALT7, XYLT1, XYLT2, EXTL3
 KEGG 6 / 24 30.3× 3.21e-8 1.99e-6 ✓ sig.
ECM proteoglycans
COL1A1, COL1A2, DSPP, SPARC, COMP, COL5A2, COL5A1
 Reactome 7 / 51 16.7× 1.80e-7 8.88e-6 ✓ sig.
Non-integrin membrane-ECM interactions
COL1A1, COL1A2, COL11A1, COL5A2, COL5A1
 Reactome 5 / 24 25.3× 1.29e-6 4.86e-5 ✓ sig.
A tetrasaccharide linker sequence is required for GAG synthesis
B3GALT6, B3GAT3, B4GALT7, XYLT1, XYLT2
 Reactome 5 / 26 23.3× 1.97e-6 6.98e-5 ✓ sig.
Collagen degradation
COL1A1, COL1A2, COL11A1, COL5A2, COL5A1, CTSK
 Reactome 6 / 52 14.0× 4.04e-6 1.29e-4 ✓ sig.
MET activates PTK2 signaling
COL1A1, COL1A2, COL11A1, COL5A2, COL5A1
 Reactome 5 / 30 20.2× 4.16e-6 1.32e-4 ✓ sig.
Extracellular matrix organization
COL1A1, COL1A2, COL5A2, COL5A1
 Reactome 4 / 15 32.4× 5.53e-6 1.66e-4 ✓ sig.
Crosslinking of collagen fibrils
BMP1, COL1A1, COL1A2, LOXL4
 Reactome 4 / 18 27.0× 1.22e-5 3.19e-4 ✓ sig.
Collagen chain trimerization
COL1A1, COL1A2, COL11A1, COL5A2, COL5A1
 Reactome 5 / 44 13.8× 2.89e-5 6.48e-4 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL1A1, COL1A2, COL11A1, COL5A2, COL5A1
 Reactome 5 / 51 11.9× 5.98e-5 1.17e-3 ✓ sig.
COPI-dependent Golgi-to-ER retrograde traffic
COPB2, KDELR2, KIF5B, NBAS, KIF22, COPB1
 Reactome 6 / 99 7.4× 1.63e-4 2.60e-3 ✓ sig.
Anchoring fibril formation
BMP1, COL1A1, COL1A2
 Reactome 3 / 15 24.3× 2.30e-4 3.41e-3 ✓ sig.
ATF6 (ATF6-alpha) activates chaperones
MBTPS2, MBTPS1
 Reactome 2 / 4 60.7× 3.99e-4 5.30e-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 ⇵
collagen fibril organization
BMP1, COL1A1, COL1A2, CRTAP, FKBP10, P3H1, P4HA1, PLOD2, PLOD3, SERPINH1, COMP, COL11A1
 GO:0030199 15 / 65 43.6× 4.02e-21 7.79e-18 ✓ sig.
bone mineralization
ALPL, COL1A2, IFITM5, TMEM38B, WNT11, COMP, FGFR3, ANKH, FGFR2
 GO:0030282 9 / 56 30.3× 1.40e-11 5.30e-9 ✓ sig.
ossification
BMP1, COL1A1, MESD, TAPT1, TMEM38B, COMP, FGFR3, SUCO, SLC34A1, CASR, THRA
 GO:0001503 11 / 110 18.9× 1.44e-11 5.45e-9 ✓ sig.
bone development
LRP5, P3H1, PLS3, PPIB, SLC10A7, TMEM38B, WNT1, TRIP11, FGFR2
 GO:0060348 9 / 76 22.4× 2.41e-10 6.69e-8 ✓ sig.
proteoglycan biosynthetic process
B3GALT6, B4GALT7, XYLT1, XYLT2, CANT1, CSGALNACT1
 GO:0030166 6 / 21 53.9× 9.65e-10 2.22e-7 ✓ sig.
chondroitin sulfate proteoglycan biosynthetic process
B3GALT6, B3GAT3, CHST3, XYLT1, XYLT2, CSGALNACT1
 GO:0050650 6 / 26 43.6× 4.01e-9 7.93e-7 ✓ sig.
skeletal system development
ALPL, BMP1, COL1A1, COL1A2, IFITM5, COMP, FGFR3, COL5A2, ANKH, TP63
 GO:0001501 10 / 151 12.5× 7.41e-9 1.36e-6 ✓ sig.
heparan sulfate proteoglycan biosynthetic process
B3GALT6, B3GAT3, XYLT1, XYLT2, CSGALNACT1, EXTL3
 GO:0015012 6 / 30 37.8× 1.02e-8 1.78e-6 ✓ sig.
bone morphogenesis
IFITM5, LRP5, COMP, FGFR3, SKI, FGFR2
 GO:0060349 6 / 32 35.4× 1.54e-8 2.57e-6 ✓ sig.
glycosaminoglycan biosynthetic process
B3GALT6, B3GAT3, B4GALT7, XYLT1, XYLT2
 GO:0006024 5 / 20 47.2× 5.49e-8 7.61e-6 ✓ sig.
glycosaminoglycan metabolic process
B3GALT6, B4GALT7, XYLT1, XYLT2
 GO:0030203 4 / 12 62.9× 3.55e-7 3.61e-5 ✓ sig.
cartilage development
BMP1, TAPT1, COMP, FGFR3, CSGALNACT1, COL11A1, TRIP11
 GO:0051216 7 / 89 14.8× 4.57e-7 4.47e-5 ✓ sig.
tendon development
COMP, COL11A1, COL5A1
 GO:0035989 3 / 4 142× 5.75e-7 5.39e-5 ✓ sig.
cementum mineralization
ALPL, SP7, ANKH
 GO:0071529 3 / 6 94.4× 2.85e-6 1.97e-4 ✓ sig.
endoplasmic reticulum to Golgi vesicle-mediated transport
COPB2, MIA3, P4HB, SEC16B, SEC24D, COPB1, TRIP11
 GO:0006888 7 / 133 9.9× 6.82e-6 3.94e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bone fragility with contractures, arterial rupture, and deafness Osteoporosis-pseudoglioma syndrome 0.980 49 3.22e-143 1.76e-141 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Osteogenesis imperfecta 0.492 30 3.20e-71 1.06e-69 ✓ sig.
Osteogenesis imperfecta Osteoporosis-pseudoglioma syndrome 0.492 30 3.20e-71 1.06e-69 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Larsen syndrome 0.155 9 3.48e-19 4.94e-18 ✓ sig.
Larsen syndrome Osteoporosis-pseudoglioma syndrome 0.155 9 3.48e-19 4.94e-18 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Skeletal dysplasia 0.095 8 5.99e-13 6.52e-12 ✓ sig.
Osteoporosis-pseudoglioma syndrome Skeletal dysplasia 0.095 8 5.99e-13 6.52e-12 ✓ sig.
Larsen syndrome Skeletal dysplasia 0.091 5 6.92e-10 6.06e-9 ✓ sig.
Cole-carpenter syndrome Osteogenesis imperfecta 0.071 3 1.72e-8 1.34e-7 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Cole-carpenter syndrome 0.060 3 2.98e-8 2.22e-7 ✓ sig.
Cole-carpenter syndrome Osteoporosis-pseudoglioma syndrome 0.060 3 2.98e-8 2.22e-7 ✓ sig.
Osteogenesis imperfecta Skeletal dysplasia 0.063 5 7.99e-8 5.68e-7 ✓ sig.
Larsen syndrome Spondyloepimetaphyseal dysplasia with joint laxity, 2 0.056 1 1.10e-3 1.65e-3 ✓ sig.
Larsen syndrome Skeletal dysplasia, mild, with joint laxity and advanced bone age 0.056 1 1.10e-3 1.65e-3 ✓ sig.
Joint laxity, short stature, and myopia Larsen syndrome 0.056 1 1.10e-3 1.65e-3 ✓ sig.
Immunoskeletal dysplasia with neurodevelopmental abnormalities Skeletal dysplasia 0.023 1 2.71e-3 3.48e-3 ✓ sig.
Dysostosis multiplex, ain-naz type Skeletal dysplasia 0.023 1 2.71e-3 3.48e-3 ✓ sig.
Skeletal dysplasia Skeletal dysplasia, mild, with joint laxity and advanced bone age 0.023 1 2.71e-3 3.48e-3 ✓ sig.
Craniotubular dysplasia Skeletal dysplasia 0.023 1 2.71e-3 3.48e-3 ✓ sig.