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 15

23 diseases · 83 shared-gene connections
23 Diseases
48 Unique genes
0.334 Avg. similarity score
Collagenopathy Most-connected disease (19 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 ⇵
Collagenopathy 19 19 1
Coxa plana 19 19 1
Czech dysplasia 18 18 1
Dysspondyloenchondromatosis 18 18 1
kniest dysplasia 15 15 1
Congenital hip dysplasia 7 7 5
Avascular necrosis of femoral head 6 6 3
COL2A1-related spondyloepiphyseal dysplasia 5 5 1
Otospondylomegaepiphyseal dysplasia 5 5 2
Rhegmatogenous retinal detachment 5 5 7
Stickler syndrome type 1 5 5 1
Synovitis 5 5 9
Vitreoretinopathy 5 5 3
achondrogenesis type II 5 5 1
dysplasia of the proximal femoral epiphyses 5 5 1
platyspondylic dysplasia, Torrance type 5 5 1
spondyloperipheral dysplasia 5 5 1
Chondrosarcoma 4 4 9
Maffucci syndrome 4 4 9
Eye disorder 3 3 10
Beukes hip dysplasia 1 1 1
GNPTAB-mucolipidosis 1 1 1
Hip dislocation-facial dysmorphism syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL2A1 20 / 23 achondrogenesis type II, Avascular necrosis of femoral head, Chondrosarcoma, COL2A1-related spondyloepiphyseal dysplasia and 16 more
GNPTAB 2 / 23 Avascular necrosis of femoral head, GNPTAB-mucolipidosis
POMC 2 / 23 Eye disorder, Synovitis
TRIM33 2 / 23 Congenital hip dysplasia, Hip dislocation-facial dysmorphism syndrome
UFSP2 2 / 23 Beukes hip dysplasia, Congenital hip 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 ⇵
Interleukin-1 processing
IL1A, IL18, IL1B
 Reactome 3 / 8 93.8× 3.31e-6 1.35e-4 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
BCL2, IL1A, IL18, IL1B, POMC, HIF1A
 Reactome 6 / 108 13.9× 4.15e-6 1.63e-4 ✓ sig.
Purinergic signaling in leishmaniasis infection
IL1A, IL18, IL1B
 Reactome 3 / 24 31.3× 1.14e-4 2.49e-3 ✓ sig.
Central carbon metabolism in cancer
PDGFRA, HIF1A, IDH1, IDH2
 KEGG 4 / 71 14.1× 1.79e-4 3.59e-3 ✓ sig.
Cellular senescence
TRPV4, IL1A, CDKN2A, HLA-B, IGFBP3
 KEGG 5 / 157 8.0× 3.90e-4 6.58e-3 ✓ sig.
Type I diabetes mellitus
IL1A, IL1B, HLA-B
 KEGG 3 / 44 17.1× 7.07e-4 1.04e-2 ✓ sig.
Graft-versus-host disease
IL1A, IL1B, HLA-B
 KEGG 3 / 45 16.7× 7.56e-4 1.10e-2 ✓ sig.
Interleukin-10 signaling
IL1A, IL18, IL1B
 Reactome 3 / 47 16.0× 8.59e-4 1.21e-2 ✓ sig.
Human cytomegalovirus infection
PDGFRA, IL1B, CDKN2A, CREB5, HLA-B
 KEGG 5 / 226 5.5× 2.00e-3 2.28e-2 ✓ sig.
Inflammatory bowel disease
IL1A, IL18, IL1B
 KEGG 3 / 66 11.4× 2.30e-3 2.53e-2 ✓ sig.
Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
PSMC3, HIF1A, VHL
 Reactome 3 / 66 11.4× 2.30e-3 2.53e-2 ✓ sig.
Fluid shear stress and atherosclerosis
TRPV4, BCL2, IL1A, IL1B
 KEGG 4 / 141 7.1× 2.37e-3 2.59e-2 ✓ sig.
Renal cell carcinoma
HIF1A, PTPN11, VHL
 KEGG 3 / 70 10.7× 2.72e-3 2.87e-2 ✓ sig.
Biosynthesis of amino acids
IDH1, IDH2, PYCR3
 KEGG 3 / 75 10.0× 3.31e-3 3.30e-2 ✓ sig.
p53 signaling pathway
BCL2, CDKN2A, IGFBP3
 KEGG 3 / 75 10.0× 3.31e-3 3.30e-2 ✓ 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 ⇵
cartilage development involved in endochondral bone morphogenesis
COL2A1, TRPV4, EXT1
 GO:0060351 3 / 9 130× 1.32e-6 1.03e-4 ✓ sig.
extrinsic apoptotic signaling pathway in absence of ligand
COL2A1, BCL2, IL1A, IL1B
 GO:0097192 4 / 36 43.3× 2.12e-6 1.51e-4 ✓ sig.
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
COL2A1, BCL2, IL1A, IL1B
 GO:2001240 4 / 37 42.1× 2.38e-6 1.65e-4 ✓ sig.
glyoxylate cycle
IDH1, IDH2
 GO:0006097 2 / 2 389× 6.46e-6 3.68e-4 ✓ sig.
retina vasculature development in camera-type eye
PDGFRA, HIF1A, LRP5
 GO:0061298 3 / 15 77.9× 7.08e-6 3.97e-4 ✓ sig.
positive regulation of transcription by RNA polymerase II
NR4A3, IL1A, PSMC3, IL18, IL1B, POMC, CDKN2A, HIF1A, KDM4C, LDB2, SS18, WWP2
 GO:0045944 13 / 1,208 4.2× 7.41e-6 4.11e-4 ✓ sig.
regulation of gene expression
COL2A1, BCL2, F2, CDKN2A, HIF1A, KDM4C, VHL, RELN
 GO:0010468 8 / 402 7.7× 7.60e-6 4.20e-4 ✓ sig.
cell morphogenesis
EXT1, BCL2, VHL, SS18, RELN
 GO:0000902 5 / 119 16.4× 1.32e-5 6.50e-4 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
PDGFRA, F2, IL18, IL1B, PTPN11, RELN
 GO:0051897 6 / 217 10.8× 1.87e-5 8.50e-4 ✓ sig.
dendritic cell apoptotic process
NR4A3, BCL2
 GO:0097048 2 / 3 260× 1.94e-5 8.74e-4 ✓ sig.
fever generation
IL1A, IL1B
 GO:0001660 2 / 3 260× 1.94e-5 8.74e-4 ✓ sig.
glucose homeostasis
TRPV4, POMC, CDKN2A, HIF1A, PTPN11
 GO:0042593 5 / 134 14.5× 2.35e-5 1.02e-3 ✓ sig.
negative regulation of proteolysis involved in protein catabolic process
UFSP2, CDKN2A
 GO:1903051 2 / 4 195× 3.86e-5 1.48e-3 ✓ sig.
negative regulation of ossification
BCL2, HIF1A, LRP4
 GO:0030279 3 / 27 43.3× 4.45e-5 1.65e-3 ✓ sig.
positive regulation of mitotic nuclear division
IL1A, IL1B, LRP5
 GO:0045840 3 / 29 40.3× 5.55e-5 1.95e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Eye disorder Synovitis 0.111 2 1.36e-5 6.99e-5 ✓ sig.
Dysspondyloenchondromatosis spondyloperipheral dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana Czech dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana spondyloperipheral dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Czech dysplasia Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Czech dysplasia kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Czech dysplasia spondyloperipheral dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy dysplasia of the proximal femoral epiphyses 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana dysplasia of the proximal femoral epiphyses 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Czech dysplasia dysplasia of the proximal femoral epiphyses 0.500 1 6.49e-5 2.34e-4 ✓ sig.
dysplasia of the proximal femoral epiphyses Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
dysplasia of the proximal femoral epiphyses kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dysspondyloenchondromatosis kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
achondrogenesis type II Coxa plana 0.500 1 6.49e-5 2.34e-4 ✓ sig.
kniest dysplasia spondyloperipheral dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Czech dysplasia platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dysspondyloenchondromatosis platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.34e-4 ✓ sig.
kniest dysplasia platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy Stickler syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana Stickler syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Czech dysplasia Stickler syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dysspondyloenchondromatosis Stickler syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
kniest dysplasia Stickler syndrome type 1 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy Coxa plana 0.500 1 6.49e-5 2.34e-4 ✓ sig.
achondrogenesis type II kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
achondrogenesis type II Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
achondrogenesis type II Czech dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
achondrogenesis type II Collagenopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Collagenopathy 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Coxa plana 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Czech dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy Czech dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy kniest dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Collagenopathy spondyloperipheral dysplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Coxa plana Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
kniest dysplasia Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dysspondyloenchondromatosis Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Czech dysplasia Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Collagenopathy Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Avascular necrosis of femoral head Collagenopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Avascular necrosis of femoral head Coxa plana 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Avascular necrosis of femoral head Czech dysplasia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Avascular necrosis of femoral head Dysspondyloenchondromatosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Avascular necrosis of femoral head kniest dysplasia 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Collagenopathy Vitreoretinopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Coxa plana Vitreoretinopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Czech dysplasia Vitreoretinopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Dysspondyloenchondromatosis Vitreoretinopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
kniest dysplasia Vitreoretinopathy 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Avascular necrosis of femoral head GNPTAB-mucolipidosis 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital hip dysplasia Czech dysplasia 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital hip dysplasia Dysspondyloenchondromatosis 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Beukes hip dysplasia Congenital hip dysplasia 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital hip dysplasia kniest dysplasia 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital hip dysplasia Coxa plana 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital hip dysplasia Hip dislocation-facial dysmorphism syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Collagenopathy Congenital hip dysplasia 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Coxa plana Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.55e-4 ✓ sig.
kniest dysplasia Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Dysspondyloenchondromatosis Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Czech dysplasia Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Collagenopathy Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Czech dysplasia Maffucci syndrome 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Dysspondyloenchondromatosis Synovitis 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Czech dysplasia Synovitis 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Coxa plana Synovitis 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Collagenopathy Synovitis 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Chondrosarcoma Dysspondyloenchondromatosis 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Chondrosarcoma Czech dysplasia 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Chondrosarcoma Coxa plana 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Chondrosarcoma Collagenopathy 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Collagenopathy Maffucci syndrome 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Coxa plana Maffucci syndrome 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Dysspondyloenchondromatosis Maffucci syndrome 0.100 1 5.84e-4 1.14e-3 ✓ sig.
Collagenopathy Eye disorder 0.091 1 6.49e-4 1.22e-3 ✓ sig.
Coxa plana Eye disorder 0.091 1 6.49e-4 1.22e-3 ✓ sig.