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 93

12 diseases · 26 shared-gene connections
12 Diseases
38 Unique genes
0.306 Avg. similarity score
Caffey disease Most-connected disease (7 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 ⇵
Caffey disease 7 7 1
Maternal hypertension 7 7 1
Rhizomelia 7 7 1
COL1A1-related Ehlers-Danlos syndrome 6 6 1
Combined osteogenesis imperfecta and ehlers-danlos syndrome 6 6 2
Cortical congenital hyperostosis 5 5 2
Dermatofibrosarcoma protuberans 5 5 2
Cholangitis 3 3 14
Skeletal dysplasia 3 3 23
A4GALT-congenital disorder of glycosylation 1 1 1
Craniotubular dysplasia 1 1 1
immunoskeletal dysplasia with neurodevelopmental abnormalities 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL1A1 9 / 12 Caffey disease, Cholangitis, COL1A1-related Ehlers-Danlos syndrome, Combined osteogenesis imperfecta and ehlers-danlos syndrome and 5 more
A4GALT 2 / 12 A4GALT-congenital disorder of glycosylation, Cortical congenital hyperostosis
COL1A2 2 / 12 Combined osteogenesis imperfecta and ehlers-danlos syndrome , Skeletal dysplasia
EXTL3 2 / 12 immunoskeletal dysplasia with neurodevelopmental abnormalities, Skeletal dysplasia
TMEM53 2 / 12 Craniotubular dysplasia, Skeletal dysplasia
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
COL1A1, COL1A2, PDGFB, COL5A1
 Reactome 4 / 24 52.7× 8.65e-7 4.30e-5 ✓ sig.
Extracellular matrix organization
COL1A1, COL1A2, COL5A1
 Reactome 3 / 15 63.2× 1.30e-5 4.16e-4 ✓ sig.
ECM proteoglycans
COL1A1, ITGB6, COL1A2, COL5A1
 Reactome 4 / 51 24.8× 1.91e-5 5.78e-4 ✓ sig.
Collagen degradation
COL1A1, COL1A2, COL5A1, CTSK
 Reactome 4 / 52 24.3× 2.07e-5 6.15e-4 ✓ sig.
Crosslinking of collagen fibrils
COL1A1, COL1A2, LOXL4
 Reactome 3 / 18 52.7× 2.31e-5 6.71e-4 ✓ sig.
MET activates PTK2 signaling
COL1A1, COL1A2, COL5A1
 Reactome 3 / 30 31.6× 1.12e-4 2.46e-3 ✓ sig.
Integrin cell surface interactions
COL1A1, ITGB6, COL1A2, COL5A1
 Reactome 4 / 81 15.6× 1.19e-4 2.58e-3 ✓ sig.
Platelet Aggregation (Plug Formation)
COL1A1, COL1A2
 Reactome 2 / 8 79.0× 2.70e-4 4.94e-3 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications
COL1A1, EGR1, TGFB2, COL1A2
 KEGG 4 / 101 12.5× 2.79e-4 5.08e-3 ✓ sig.
Amoebiasis
COL1A1, TGFB2, NOS2, COL1A2
 KEGG 4 / 103 12.3× 3.01e-4 5.38e-3 ✓ sig.
Collagen chain trimerization
COL1A1, COL1A2, COL5A1
 Reactome 3 / 44 21.5× 3.54e-4 6.10e-3 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
TIMP1, HIF1A, NOS2, COL1A2
 Reactome 4 / 108 11.7× 3.61e-4 6.19e-3 ✓ sig.
Platelet Adhesion to exposed collagen
COL1A1, COL1A2
 Reactome 2 / 11 57.5× 5.27e-4 8.28e-3 ✓ sig.
Assembly of collagen fibrils and other multimeric structures
COL1A1, COL1A2, COL5A1
 Reactome 3 / 51 18.6× 5.48e-4 8.54e-3 ✓ sig.
GP1b-IX-V activation signalling
COL1A1, COL1A2
 Reactome 2 / 12 52.7× 6.31e-4 9.56e-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
COL1A1, TGFB2, COL1A2, COL5A1, LOXL4
 GO:0030199 5 / 65 37.8× 2.00e-7 2.17e-5 ✓ sig.
blood vessel development
COL1A1, TGFB2, HIF1A, COL1A2, COL5A1
 GO:0001568 5 / 70 35.1× 2.91e-7 2.97e-5 ✓ sig.
skeletal system development
COL1A1, TGFB2, COL1A2, ANKH, FGFR3, TP63
 GO:0001501 6 / 151 19.5× 5.62e-7 5.16e-5 ✓ sig.
skin morphogenesis
COL1A1, COL1A2, TP63
 GO:0043589 3 / 13 113× 2.19e-6 1.55e-4 ✓ sig.
cellular response to mycophenolic acid
EGR1, PDGFB
 GO:0071506 2 / 2 492× 4.03e-6 2.53e-4 ✓ sig.
positive regulation of miRNA transcription
EGR1, TGFB2, HIF1A, PDGFB
 GO:1902895 4 / 56 35.1× 4.95e-6 2.98e-4 ✓ sig.
bone mineralization
HIF1A, COL1A2, ANKH, FGFR3
 GO:0030282 4 / 56 35.1× 4.95e-6 2.98e-4 ✓ sig.
positive regulation of hormone biosynthetic process
EGR1, HIF1A
 GO:0046886 2 / 3 328× 1.21e-5 6.03e-4 ✓ sig.
regulation of transforming growth factor beta2 production
TGFB2, HIF1A
 GO:0032909 2 / 4 246× 2.41e-5 1.03e-3 ✓ sig.
response to hypoxia
EGR1, TGFB2, HIF1A, NOS2, TRPV4
 GO:0001666 5 / 176 14.0× 2.73e-5 1.14e-3 ✓ sig.
cartilage development
TIMP1, HIF1A, FGFR3, CSGALNACT1
 GO:0051216 4 / 89 22.1× 3.14e-5 1.26e-3 ✓ sig.
endochondral ossification
COL1A1, FGFR3, CSGALNACT1
 GO:0001958 3 / 31 47.6× 3.35e-5 1.33e-3 ✓ sig.
connective tissue replacement involved in inflammatory response wound healing
TIMP1, HIF1A
 GO:0002248 2 / 5 197× 4.01e-5 1.52e-3 ✓ sig.
neural crest cell migration
HIF1A, SEMA3A, SEMA3D
 GO:0001755 3 / 47 31.4× 1.18e-4 3.43e-3 ✓ sig.
cartilage development involved in endochondral bone morphogenesis
COL1A1, TRPV4
 GO:0060351 2 / 9 109× 1.44e-4 3.97e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Combined osteogenesis imperfecta and ehlers-danlos syndrome Skeletal dysplasia 0.083 2 2.13e-6 1.25e-5 ✓ sig.
Caffey disease Maternal hypertension 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Maternal hypertension Rhizomelia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL1A1-related Ehlers-Danlos syndrome Rhizomelia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL1A1-related Ehlers-Danlos syndrome Maternal hypertension 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Caffey disease Rhizomelia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Caffey disease COL1A1-related Ehlers-Danlos syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cortical congenital hyperostosis Maternal hypertension 0.333 1 1.30e-4 3.90e-4 ✓ sig.
A4GALT-congenital disorder of glycosylation Cortical congenital hyperostosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
COL1A1-related Ehlers-Danlos syndrome Dermatofibrosarcoma protuberans 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dermatofibrosarcoma protuberans Rhizomelia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dermatofibrosarcoma protuberans Maternal hypertension 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Caffey disease Dermatofibrosarcoma protuberans 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Cortical congenital hyperostosis Rhizomelia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Caffey disease Cortical congenital hyperostosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Rhizomelia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Maternal hypertension 0.333 1 1.30e-4 3.90e-4 ✓ sig.
COL1A1-related Ehlers-Danlos syndrome Cortical congenital hyperostosis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
COL1A1-related Ehlers-Danlos syndrome Combined osteogenesis imperfecta and ehlers-danlos syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Caffey disease Combined osteogenesis imperfecta and ehlers-danlos syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Combined osteogenesis imperfecta and ehlers-danlos syndrome Dermatofibrosarcoma protuberans 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Cholangitis Rhizomelia 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Cholangitis Maternal hypertension 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Caffey disease Cholangitis 0.067 1 9.09e-4 1.56e-3 ✓ sig.
Craniotubular dysplasia Skeletal dysplasia 0.042 1 1.49e-3 2.29e-3 ✓ sig.
immunoskeletal dysplasia with neurodevelopmental abnormalities Skeletal dysplasia 0.042 1 1.49e-3 2.29e-3 ✓ sig.