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 153

10 diseases · 13 shared-gene connections
10 Diseases
359 Unique genes
0.029 Avg. similarity score
Bone fracture Most-connected disease (6 links)
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Disease Searched: Autosomal recessive osteopetrosis 5 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 ⇵
Bone fracture 6 6 68
Bone disease 4 4 83
Dupuytren contracture 4 4 89
Osteoporosis 4 4 161
Marbach-schaaf neurodevelopmental syndrome 2 2 1
Temtamy preaxial brachydactyly syndrome 2 2 1
Amyotrophic lateral sclerosis type 18 1 1 1
Autosomal recessive osteopetrosis 5 1 1 1
Parkinsonism with polyneuropathy 1 1 1
Succinyl-coa:3-oxoacid coa transferase deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SFRP4 4 / 10 Bone disease, Bone fracture, Dupuytren contracture, Osteoporosis
STARD3NL 4 / 10 Bone disease, Bone fracture, Dupuytren contracture, Osteoporosis
AXIN1 3 / 10 Bone disease, Bone fracture, Osteoporosis
CCDC170 3 / 10 Bone disease, Bone fracture, Osteoporosis
CHSY1 3 / 10 Bone fracture, Dupuytren contracture, Temtamy preaxial brachydactyly syndrome
CYP19A1 3 / 10 Bone disease, Bone fracture, Osteoporosis
ESR1 3 / 10 Bone disease, Bone fracture, Osteoporosis
FMN2 3 / 10 Bone disease, Bone fracture, Dupuytren contracture
PRKAR1B 3 / 10 Bone fracture, Dupuytren contracture, Marbach-schaaf neurodevelopmental syndrome
RSPO3 3 / 10 Bone disease, Bone fracture, Osteoporosis
SEM1 3 / 10 Bone disease, Bone fracture, Osteoporosis
ZBTB40 3 / 10 Bone disease, Dupuytren contracture, Osteoporosis
ALDH7A1 2 / 10 Bone disease, Osteoporosis
AQP1 2 / 10 Bone fracture, Osteoporosis
BMP2 2 / 10 Bone disease, Osteoporosis
DDN 2 / 10 Bone disease, Osteoporosis
DOK6 2 / 10 Bone fracture, Osteoporosis
FAM3C 2 / 10 Bone disease, Osteoporosis
HLA-DQA1 2 / 10 Bone disease, Osteoporosis
HLA-DRB1 2 / 10 Bone disease, Osteoporosis
JAG1 2 / 10 Bone disease, Dupuytren contracture
LEPR 2 / 10 Bone disease, Osteoporosis
LRP5 2 / 10 Bone fracture, Osteoporosis
OSTM1 2 / 10 Autosomal recessive osteopetrosis 5, Osteoporosis
OXCT1 2 / 10 Osteoporosis, Succinyl-coa:3-oxoacid coa transferase deficiency
PFN1 2 / 10 Amyotrophic lateral sclerosis type 18, Bone disease
PPP6R3 2 / 10 Bone disease, Osteoporosis
PTH 2 / 10 Bone disease, Osteoporosis
RAB31 2 / 10 Bone fracture, Dupuytren contracture
SOX6 2 / 10 Bone fracture, Osteoporosis
SUPT3H 2 / 10 Bone disease, Bone fracture
UQCRC1 2 / 10 Bone fracture, Parkinsonism with polyneuropathy
WNT1 2 / 10 Bone disease, Osteoporosis
WNT16 2 / 10 Bone fracture, Osteoporosis
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 ⇵
Proteoglycans in cancer
WNT1, ESR1, FGF2, MMP2, ANK1, IGF2, TGFB2, IGF1, FZD7, ITGA2, ITGB3, WNT16
 KEGG 27 / 204 4.4× 7.40e-11 9.01e-9 ✓ sig.
Wnt signaling pathway
LRP5, AXIN1, RSPO3, SFRP4, TCF7L2, WNT1, FZD7, NFATC1, SOST, WNT16, NFATC2, RSPO2
 KEGG 21 / 174 4.0× 5.22e-8 3.16e-6 ✓ sig.
Pathways in cancer
LRP5, ABL1, AXIN1, TCF7L2, WNT1, BMP2, CDKN2A, ESR1, FGF2, JAG1, MMP2, TGFBR2
 KEGG 40 / 533 2.5× 7.05e-8 4.11e-6 ✓ sig.
Breast cancer
LRP5, TNFSF11, AXIN1, TCF7L2, WNT1, ESR1, FGF2, JAG1, IGF1, FZD7, WNT16, MTOR
 KEGG 19 / 148 4.3× 8.45e-8 4.82e-6 ✓ sig.
p130Cas linkage to MAPK signaling for integrins
ITGB3, PTK2, FGA, FGB, RAP1A, SRC, TLN1
 Reactome 7 / 15 15.6× 1.05e-7 5.85e-6 ✓ sig.
GRB2:SOS provides linkage to MAPK signaling for Integrins
ITGB3, PTK2, FGA, FGB, RAP1A, SRC, TLN1
 Reactome 7 / 15 15.6× 1.05e-7 5.85e-6 ✓ sig.
Integrin signaling
ITGB3, PTK2, RASGRP2, FGA, FGB, RAP1A, SRC, TLN1
 Reactome 8 / 23 11.6× 1.95e-7 1.00e-5 ✓ sig.
Platelet degranulation
FAM3C, IGF2, TGFB2, PDGFA, IGF1, ITGB3, CD36, FERMT3, FGA, FGB, PLEK, SPP2
 Reactome 16 / 123 4.4× 7.50e-7 3.25e-5 ✓ sig.
Hepatocellular carcinoma
LRP5, AXIN1, TCF7L2, WNT1, CDKN2A, TGFBR2, IGF2, TGFB2, FZD7, WNT16, MTOR, WNT2
 KEGG 19 / 170 3.7× 7.59e-7 3.28e-5 ✓ sig.
Basal cell carcinoma
AXIN1, TCF7L2, WNT1, BMP2, FZD7, WNT16, WNT2, WNT7B, WNT3A, BMP4, WNT11
 KEGG 11 / 63 5.8× 2.23e-6 8.28e-5 ✓ sig.
Inflammatory bowel disease
HLA-DQA1, HLA-DRB1, TGFB2, MAF, NFATC1, HLA-DRB5, IL1A, IL6, TGFB1, IL1B, TNF
 KEGG 11 / 66 5.6× 3.59e-6 1.25e-4 ✓ sig.
Cushing syndrome
AXIN1, TCF7L2, WNT1, AHR, CDKN2A, FZD7, WNT16, ADCY4, WNT2, WNT7B, WNT3A, ADCY5
 KEGG 17 / 155 3.7× 3.78e-6 1.30e-4 ✓ sig.
Hippo signaling pathway
AXIN1, TCF7L2, WNT1, BMP2, TGFBR2, BMPR1B, TGFB2, FZD7, WNT16, LIMD1, WNT2, WNT7B
 KEGG 17 / 157 3.6× 4.50e-6 1.51e-4 ✓ sig.
Rheumatoid arthritis
TCIRG1, TNFSF11, TNFRSF11A, HLA-DQA1, HLA-DRB1, TGFB2, PTH, HLA-DRB5, IL1A, IL6, TGFB1, IL1B
 KEGG 13 / 95 4.6× 4.66e-6 1.55e-4 ✓ sig.
Fluid shear stress and atherosclerosis
MMP2, TRPV4, BMPR1B, CHUK, NPPC, PDGFA, ITGB3, KDR, PTK2, ACTG1, BMP4, GSTP1
 KEGG 16 / 141 3.8× 4.68e-6 1.56e-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 ⇵
skeletal system development
SFRP4, BMP2, LTBP3, DLX5, IFT80, RPS6KA3, SH3PXD2B, TGFB2, TRPS1, ZIC3, PTH, ALPL
 GO:0001501 25 / 151 8.6× 1.39e-16 1.33e-13 ✓ sig.
ossification
TCIRG1, TNFSF11, TNFRSF11A, BMP2, CBFB, DLX5, IFT80, IGF2, NPPC, SLC34A1, TMCO1, EXT1
 GO:0001503 22 / 110 10.4× 1.49e-16 1.42e-13 ✓ sig.
osteoblast differentiation
BMP2, FGF2, BMPR1B, CBFB, DLX5, IFT80, IGF2, ALPL, IGF1, ITGA11, RSPO2, TNC
 GO:0001649 23 / 137 8.7× 1.72e-15 1.36e-12 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
TNFSF11, TCF7L2, FGF2, PTK2B, IGF2, ITGB1BP1, TGFB2, PDGFA, IGF1, ADTRP, WNT16, DDR2
 GO:0051897 27 / 217 6.5× 1.29e-14 8.66e-12 ✓ sig.
canonical Wnt signaling pathway
LRP5, AXIN1, RSPO3, SFRP4, TCF7L2, WNT1, FGF2, EXT1, FZD7, SOST, WNT16, RSPO2
 GO:0060070 19 / 105 9.4× 1.24e-13 7.02e-11 ✓ sig.
positive regulation of ERK1 and ERK2 cascade
TNFSF11, TNFRSF11A, ABL1, HLA-DRB1, BMP2, FGF2, PTK2B, TRPV4, PDGFA, IGF1, ITGB3, DDR2
 GO:0070374 25 / 201 6.5× 1.28e-13 7.22e-11 ✓ sig.
positive regulation of transcription by RNA polymerase II
LRP5, TNFSF11, ABL1, CDC5L, DAB2IP, DDN, TCF7L2, WNT1, AHR, BMP2, CDKN2A, ESR1
 GO:0045944 63 / 1,208 2.7× 3.08e-13 1.62e-10 ✓ sig.
positive regulation of osteoblast differentiation
LRP5, BMP2, FGF2, JAG1, BMPR1B, NPPC, IGF1, TENT5A, DDR2, SFRP2, WNT7B, BMP4
 GO:0045669 15 / 78 10.0× 1.95e-11 6.94e-9 ✓ sig.
bone mineralization
ZBTB40, BMP2, LTBP3, PTH, ALPL, PHOSPHO1, FGFR2, RSPO2, BGLAP, COL1A2, IFITM5, WNT11
 GO:0030282 13 / 56 12.1× 3.51e-11 1.19e-8 ✓ sig.
response to activity
MMP2, ITGB3, UQCRC1, ANXA2, BGLAP, IL6, KL, LEP, OXCT1, SOD2, CAT, TNF
 GO:0014823 12 / 52 12.0× 2.18e-10 6.14e-8 ✓ sig.
positive regulation of gene expression
TNFSF11, SFRP4, BMP2, CDKN2A, FGF2, TRPV4, BMPR1B, DLX5, TGFB2, PTH, IGF1, ADTRP
 GO:0010628 34 / 504 3.5× 2.28e-10 6.39e-8 ✓ sig.
positive regulation of cell population proliferation
LRP5, TCIRG1, TNFRSF11A, WNT1, BMP2, FGF2, LEPR, PTK2B, TGFBR2, IGF2, ITGB1BP1, TGFB2
 GO:0008284 35 / 532 3.4× 2.40e-10 6.72e-8 ✓ sig.
bone morphogenesis
LRP5, SFRP4, LTBP3, DLX5, IFT80, CHSY1, EXT1, FGFR2, LTF, IFITM5
 GO:0060349 10 / 32 16.3× 2.68e-10 7.39e-8 ✓ sig.
cellular response to retinoic acid
PTK2B, AQP1, FZD7, FGFR2, TNC, WNT2, WNT7B, WNT3A, COL1A1, LEP, SERPINF1, TNF
 GO:0071300 13 / 69 9.8× 5.73e-10 1.44e-7 ✓ sig.
osteoclast differentiation
SNX10, TCIRG1, TNFSF11, OSTM1, TNFRSF11A, BMP2, IFT80, SLC4A2, CALCR, TGFB1, TNF
 GO:0030316 11 / 49 11.7× 1.71e-9 3.71e-7 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bone disease Osteoporosis 0.084 19 1.02e-20 1.53e-19 ✓ sig.
Bone fracture Osteoporosis 0.060 13 1.94e-13 2.18e-12 ✓ sig.
Bone disease Bone fracture 0.070 10 2.53e-12 2.64e-11 ✓ sig.
Bone fracture Dupuytren contracture 0.039 6 2.50e-6 1.44e-5 ✓ sig.
Bone disease Dupuytren contracture 0.030 5 1.14e-4 3.27e-4 ✓ sig.
Bone fracture Marbach-schaaf neurodevelopmental syndrome 0.014 1 4.39e-3 5.34e-3 ✓ sig.
Bone fracture Parkinsonism with polyneuropathy 0.014 1 4.39e-3 5.34e-3 ✓ sig.
Bone fracture Temtamy preaxial brachydactyly syndrome 0.014 1 4.39e-3 5.34e-3 ✓ sig.
Amyotrophic lateral sclerosis type 18 Bone disease 0.012 1 5.36e-3 6.37e-3 ✓ sig.
Dupuytren contracture Marbach-schaaf neurodevelopmental syndrome 0.011 1 5.75e-3 6.78e-3 ✓ sig.
Dupuytren contracture Temtamy preaxial brachydactyly syndrome 0.011 1 5.75e-3 6.78e-3 ✓ sig.
Autosomal recessive osteopetrosis 5 Osteoporosis 0.006 1 1.04e-2 1.16e-2 ✓ sig.
Osteoporosis Succinyl-coa:3-oxoacid coa transferase deficiency 0.006 1 1.04e-2 1.16e-2 ✓ sig.