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 11

25 diseases · 81 shared-gene connections
25 Diseases
79 Unique genes
0.317 Avg. similarity score
Collagenopathy Most-connected disease (18 links)
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Disease Searched: platyspondylic dysplasia, Torrance type 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 18 18 1
Coxa plana 18 18 1
Czech dysplasia 17 17 1
Dysspondyloenchondromatosis 17 17 1
kniest dysplasia 14 14 1
Congenital hip dysplasia 7 7 5
Avascular necrosis of femoral head 6 6 3
Rhegmatogenous retinal detachment 6 6 7
Vitreoretinopathy 6 6 3
COL2A1-related spondyloepiphyseal dysplasia 5 5 1
Otospondylomegaepiphyseal dysplasia 5 5 2
Stickler syndrome type 1 5 5 1
Synovitis 5 5 9
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
Synovial sarcoma 2 2 3
Beukes hip dysplasia 1 1 1
GNPTAB-mucolipidosis 1 1 1
Hip dislocation-facial dysmorphism syndrome 1 1 1
Neovascular inflammatory vitreoretinopathy 1 1 1
Sarcoma 1 1 33

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL2A1 19 / 25 Avascular necrosis of femoral head, Chondrosarcoma, COL2A1-related spondyloepiphyseal dysplasia, Collagenopathy and 15 more
SS18 3 / 25 Rhegmatogenous retinal detachment, Sarcoma, Synovial sarcoma
BCL2 2 / 25 Chondrosarcoma, Sarcoma
CAPN5 2 / 25 Neovascular inflammatory vitreoretinopathy, Vitreoretinopathy
GNPTAB 2 / 25 Avascular necrosis of femoral head, GNPTAB-mucolipidosis
POMC 2 / 25 Eye disorder, Synovitis
SSX1 2 / 25 Sarcoma, Synovial sarcoma
SSX2 2 / 25 Sarcoma, Synovial sarcoma
TRIM33 2 / 25 Congenital hip dysplasia, Hip dislocation-facial dysmorphism syndrome
UFSP2 2 / 25 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-4 and Interleukin-13 signaling
BCL2, IL1A, IL18, IL1B, POMC, HIF1A, MCL1, SOX2, TNF, TP53, IL6, VIM
 Reactome 12 / 108 16.9× 4.65e-12 8.90e-10 ✓ sig.
Transcriptional misregulation in cancer
NR4A3, TAF15, SS18, ATM, CSF2, PAX3, TP53, ASPSCR1, EWSR1, FLI1, IL6, SSX1
 KEGG 14 / 198 10.7× 3.36e-11 5.47e-9 ✓ sig.
Cellular senescence
TRPV4, IL1A, CDKN2A, ATM, ATR, PIK3CA, TP53, IL6, HLA-B, IGFBP3
 KEGG 10 / 157 9.7× 7.27e-8 5.28e-6 ✓ sig.
Human T-cell leukemia virus 1 infection
CDKN2A, ATM, ATR, CSF2, PIK3CA, TNF, TP53, EGR2, IL6, CREB5, HLA-B
 KEGG 11 / 224 7.5× 2.21e-7 1.39e-5 ✓ sig.
Fluid shear stress and atherosclerosis
TRPV4, BCL2, IL1A, IL1B, GSTP1, IFNG, PIK3CA, TNF, TP53
 KEGG 9 / 141 9.7× 3.36e-7 2.02e-5 ✓ sig.
Graft-versus-host disease
IL1A, IL1B, IFNG, TNF, IL6, HLA-B
 KEGG 6 / 45 20.3× 4.44e-7 2.57e-5 ✓ sig.
Interleukin-10 signaling
IL1A, IL18, IL1B, CSF2, TNF, IL6
 Reactome 6 / 47 19.4× 5.79e-7 3.22e-5 ✓ sig.
Rheumatoid arthritis
IL1A, IL18, IL1B, CSF2, IFNG, TNF, IL6
 KEGG 7 / 95 11.2× 2.82e-6 1.27e-4 ✓ sig.
Herpes simplex virus 1 infection
BCL2, IL1B, PTPN11, IFNG, PIK3CA, TNF, TP53, IL6, HLA-B
 KEGG 9 / 182 7.5× 2.86e-6 1.29e-4 ✓ sig.
African trypanosomiasis
IL18, IL1B, IFNG, TNF, IL6
 KEGG 5 / 37 20.5× 4.01e-6 1.70e-4 ✓ sig.
Inflammatory bowel disease
IL1A, IL18, IL1B, IFNG, TNF, IL6
 KEGG 6 / 66 13.8× 4.44e-6 1.85e-4 ✓ sig.
Central carbon metabolism in cancer
PDGFRA, HIF1A, IDH1, IDH2, PIK3CA, TP53
 KEGG 6 / 71 12.8× 6.81e-6 2.60e-4 ✓ sig.
Pathways in cancer
BCL2, PDGFRA, F2, CDKN2A, HIF1A, VHL, APC, BRCA2, GSTP1, IFNG, PIK3CA, TP53
 KEGG 14 / 533 4.0× 8.42e-6 3.09e-4 ✓ sig.
Platinum drug resistance
BCL2, CDKN2A, ATM, GSTP1, PIK3CA, TP53
 KEGG 6 / 75 12.2× 9.38e-6 3.36e-4 ✓ sig.
p53 signaling pathway
BCL2, CDKN2A, ATM, ATR, TP53, IGFBP3
 KEGG 6 / 75 12.2× 9.38e-6 3.36e-4 ✓ 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 ⇵
positive regulation of transcription by RNA polymerase II
NR4A3, IL1A, PSMC3, IL18, IL1B, POMC, CDKN2A, HIF1A, KDM4C, LDB2, SS18, ATM
 GO:0045944 26 / 1,208 5.1× 1.71e-12 7.53e-10 ✓ sig.
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
COL2A1, BCL2, IL1A, IL1B, CSF2, MCL1, TNF
 GO:2001240 7 / 37 44.8× 1.71e-10 4.72e-8 ✓ sig.
positive regulation of DNA-templated transcription
NR4A3, TAF15, IL1B, CDKN2A, HIF1A, VHL, BRCA2, HNF1B, PAX3, SMARCA4, SOX2, TNF
 GO:0045893 19 / 778 5.8× 3.97e-10 9.93e-8 ✓ sig.
vascular endothelial growth factor production
IL1B, HIF1A, TNF, IL6
 GO:0010573 4 / 6 158× 4.41e-9 8.29e-7 ✓ sig.
extrinsic apoptotic signaling pathway in absence of ligand
COL2A1, BCL2, IL1A, IL1B, MCL1, NF1
 GO:0097192 6 / 36 39.4× 8.28e-9 1.44e-6 ✓ sig.
regulation of gene expression
COL2A1, BCL2, F2, CDKN2A, HIF1A, KDM4C, VHL, ATM, CSF2, NF1, PIK3CA, SOX2
 GO:0010468 13 / 402 7.6× 1.27e-8 2.10e-6 ✓ sig.
positive regulation of gene expression
TRPV4, IL1A, IL18, IL1B, CDKN2A, HIF1A, ATM, CSF2, HNF1B, IFNG, TNF, TP53
 GO:0010628 14 / 504 6.6× 2.25e-8 3.46e-6 ✓ sig.
positive regulation of chemokine production
IL18, IL1B, HIF1A, IFNG, TNF, IL6
 GO:0032722 6 / 49 29.0× 5.69e-8 7.60e-6 ✓ sig.
brain development
EXT1, RPGRIP1L, PTPN11, ATM, BRCA2, NF1, SOX2, EGR2, BPTF, RELN
 GO:0007420 10 / 244 9.7× 7.84e-8 1.00e-5 ✓ sig.
replicative senescence
CDKN2A, ATM, ATR, TP53
 GO:0090399 4 / 16 59.1× 5.18e-7 4.94e-5 ✓ sig.
positive regulation of neuroinflammatory response
IL18, IL1B, TNF, IL6
 GO:0150078 4 / 16 59.1× 5.18e-7 4.94e-5 ✓ sig.
negative regulation of transcription by RNA polymerase II
TRPV4, NR4A3, TRIM33, CDKN2A, VHL, LDB2, GSTP1, HNF1B, IFNG, SMARCA4, SOX2, TNF
 GO:0000122 17 / 1,002 4.0× 7.49e-7 6.70e-5 ✓ sig.
positive regulation of apoptotic process
BCL2, CDKN2A, APC, ATM, MCL1, NF1, TNF, TP53, IL6, IGFBP3
 GO:0043065 10 / 326 7.3× 1.13e-6 9.36e-5 ✓ sig.
cellular response to lipopolysaccharide
IL1A, IL18, IL1B, CSF2, GSTP1, TNF, IL6, VIM
 GO:0071222 8 / 187 10.1× 1.23e-6 1.01e-4 ✓ sig.
animal organ morphogenesis
BCL2, PDGFRA, FAT3, PAX3, TNF, FLI1, LRP5
 GO:0009887 7 / 130 12.7× 1.28e-6 1.04e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Sarcoma Synovial sarcoma 0.088 3 8.97e-9 7.22e-8 ✓ sig.
Eye disorder Synovitis 0.111 2 1.36e-5 6.60e-5 ✓ sig.
Czech dysplasia kniest dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
kniest dysplasia platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Dysspondyloenchondromatosis platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Czech dysplasia platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana Czech dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana kniest dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana spondyloperipheral dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Czech dysplasia Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy spondyloperipheral dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Czech dysplasia spondyloperipheral dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy dysplasia of the proximal femoral epiphyses 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana dysplasia of the proximal femoral epiphyses 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Czech dysplasia dysplasia of the proximal femoral epiphyses 0.500 1 6.49e-5 2.33e-4 ✓ sig.
dysplasia of the proximal femoral epiphyses Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
dysplasia of the proximal femoral epiphyses kniest dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Dysspondyloenchondromatosis kniest dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Dysspondyloenchondromatosis spondyloperipheral dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Coxa plana 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana platyspondylic dysplasia, Torrance type 0.500 1 6.49e-5 2.33e-4 ✓ sig.
kniest dysplasia spondyloperipheral dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
kniest dysplasia Stickler syndrome type 1 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Dysspondyloenchondromatosis Stickler syndrome type 1 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Czech dysplasia Stickler syndrome type 1 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Coxa plana Stickler syndrome type 1 0.500 1 6.49e-5 2.33e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Collagenopathy 0.500 1 6.49e-5 2.33e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Czech dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
COL2A1-related spondyloepiphyseal dysplasia kniest dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy Coxa plana 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy Czech dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy Dysspondyloenchondromatosis 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy kniest dysplasia 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Collagenopathy Stickler syndrome type 1 0.500 1 6.49e-5 2.33e-4 ✓ sig.
kniest dysplasia Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Dysspondyloenchondromatosis Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Czech dysplasia Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Coxa plana Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Collagenopathy Otospondylomegaepiphyseal dysplasia 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Avascular necrosis of femoral head Coxa plana 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Neovascular inflammatory vitreoretinopathy Vitreoretinopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Collagenopathy Vitreoretinopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Coxa plana Vitreoretinopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Czech dysplasia Vitreoretinopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Dysspondyloenchondromatosis Vitreoretinopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
kniest dysplasia Vitreoretinopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Avascular necrosis of femoral head Collagenopathy 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Avascular necrosis of femoral head Czech dysplasia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Avascular necrosis of femoral head Dysspondyloenchondromatosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Avascular necrosis of femoral head kniest dysplasia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Avascular necrosis of femoral head GNPTAB-mucolipidosis 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Congenital hip dysplasia Coxa plana 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Beukes hip dysplasia Congenital hip dysplasia 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Collagenopathy Congenital hip dysplasia 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital hip dysplasia Czech dysplasia 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital hip dysplasia kniest dysplasia 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital hip dysplasia Dysspondyloenchondromatosis 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Congenital hip dysplasia Hip dislocation-facial dysmorphism syndrome 0.167 1 3.25e-4 7.71e-4 ✓ sig.
Collagenopathy Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Coxa plana Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Czech dysplasia Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Dysspondyloenchondromatosis Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.73e-4 ✓ sig.
kniest dysplasia Rhegmatogenous retinal detachment 0.125 1 4.55e-4 9.73e-4 ✓ sig.
Czech dysplasia Maffucci syndrome 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Coxa plana Maffucci syndrome 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Collagenopathy Maffucci syndrome 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Dysspondyloenchondromatosis Synovitis 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Czech dysplasia Synovitis 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Coxa plana Synovitis 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Collagenopathy Synovitis 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Chondrosarcoma Collagenopathy 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Chondrosarcoma Coxa plana 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Chondrosarcoma Czech dysplasia 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Chondrosarcoma Dysspondyloenchondromatosis 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Dysspondyloenchondromatosis Maffucci syndrome 0.100 1 5.84e-4 1.16e-3 ✓ sig.
Coxa plana Eye disorder 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Collagenopathy Eye disorder 0.091 1 6.49e-4 1.24e-3 ✓ sig.
Rhegmatogenous retinal detachment Synovial sarcoma 0.100 1 1.36e-3 2.15e-3 ✓ sig.