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 63

14 diseases · 23 shared-gene connections
14 Diseases
290 Unique genes
0.124 Avg. similarity score
Orofacial cleft Most-connected disease (7 links)
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Disease Searched: oligodontia-cancer predisposition syndrome 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 ⇵
Orofacial cleft 7 7 156
Craniosynostosis 6 6 59
Cleft lip 5 5 37
Cleft lip and palate 5 5 15
Complete unilateral cleft lip 5 5 36
Tooth agenesis 5 5 41
Cleft palate 4 4 60
oligodontia-cancer predisposition syndrome 3 3 1
Catifa syndrome 1 1 1
Vertebral hypersegmentation with orofacial anomalies 1 1 1
Weiss-kruszka syndrome 1 1 1
craniosynostosis and dental anomalies 1 1 1
tooth agenesis, selective, 3 1 1 1
tooth agenesis, selective, 9 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MSX1 7 / 14 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 3 more
FGFR1 6 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis and 2 more
IRF6 6 / 14 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 2 more
BMP4 5 / 14 Cleft lip, Cleft lip and palate, Complete unilateral cleft lip, Orofacial cleft and 1 more
CDH1 5 / 14 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
FGF10 5 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis and 1 more
NECTIN1 5 / 14 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
TP63 5 / 14 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
AXIN2 4 / 14 Craniosynostosis, oligodontia-cancer predisposition syndrome, Orofacial cleft, Tooth agenesis
FGFR2 4 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis
FGFR3 4 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis
NOG 4 / 14 Cleft lip, Complete unilateral cleft lip, Craniosynostosis, Orofacial cleft
PTCH1 4 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis
SUMO1 4 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip, Orofacial cleft
ABCA4 3 / 14 Cleft lip, Complete unilateral cleft lip, Orofacial cleft
ARHGAP29 3 / 14 Cleft lip and palate, Cleft palate, Orofacial cleft
BHMT2 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
DLG1 3 / 14 Cleft lip and palate, Cleft palate, Orofacial cleft
FGF2 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF3 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF7 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF8 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF9 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
GDF6 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
KIF7 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
MAFB 3 / 14 Cleft lip, Complete unilateral cleft lip, Orofacial cleft
MTHFD1 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
MTHFR 3 / 14 Cleft lip, Complete unilateral cleft lip, Orofacial cleft
MTHFS 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
MTR 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
MYC 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
NOS3 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
SDC2 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
SLC19A1 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
SPRY2 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
TYMS 3 / 14 Cleft lip, Cleft palate, Complete unilateral cleft lip
AMOTL1 2 / 14 Cleft lip and palate, Orofacial cleft
BMP2 2 / 14 Craniosynostosis, Tooth agenesis
COL2A1 2 / 14 Cleft palate, Orofacial cleft
DLX4 2 / 14 Cleft lip and palate, Orofacial cleft
FGF1 2 / 14 Cleft lip, Complete unilateral cleft lip
FLNA 2 / 14 Craniosynostosis, Orofacial cleft
GDF11 2 / 14 Orofacial cleft, Vertebral hypersegmentation with orofacial anomalies
GLI3 2 / 14 Craniosynostosis, Tooth agenesis
GREM2 2 / 14 Tooth agenesis, tooth agenesis, selective, 9
IL11RA 2 / 14 Craniosynostosis, craniosynostosis and dental anomalies
LRP6 2 / 14 Orofacial cleft, Tooth agenesis
MEIS2 2 / 14 Cleft palate, Orofacial cleft
MMP9 2 / 14 Orofacial cleft, Tooth agenesis
MSX2 2 / 14 Craniosynostosis, Tooth agenesis
PAX9 2 / 14 Tooth agenesis, tooth agenesis, selective, 3
PDGFRA 2 / 14 Cleft lip and palate, Cleft palate
POMT1 2 / 14 Cleft lip, Complete unilateral cleft lip
RIC1 2 / 14 Catifa syndrome, Cleft lip and palate
RUNX2 2 / 14 Craniosynostosis, Orofacial cleft
RYK 2 / 14 Cleft palate, Orofacial cleft
TBX22 2 / 14 Cleft palate, Orofacial cleft
TCN2 2 / 14 Cleft lip, Complete unilateral cleft lip
ZNF462 2 / 14 Craniosynostosis, Weiss-kruszka 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 ⇵
Gastric cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, MYC, EGF, FZD4, TGFB1, TGFB2
 KEGG 23 / 150 6.4× 1.25e-12 2.65e-10 ✓ sig.
Pathways in cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, MYC, PTCH1, CHUK
 KEGG 41 / 533 3.2× 3.67e-11 5.91e-9 ✓ sig.
Hippo signaling pathway
MYC, DLG1, FZD4, GDF6, TGFB1, TGFB2, TGFB3, BMP4, CDH1, FGF1, BMP2, AXIN2
 KEGG 21 / 157 5.5× 1.74e-10 2.43e-8 ✓ sig.
TGF-beta signaling pathway
MYC, GDF6, TGFB1, TGFB2, TGFB3, BMP4, NOG, BMP2, SMAD6, FBN1, TGFBR1, GREM2
 KEGG 17 / 108 6.5× 7.70e-10 9.20e-8 ✓ sig.
Activated point mutants of FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 17 19.5× 2.11e-9 2.29e-7 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, EGF, PDGFRA, FGF1
 Reactome 14 / 75 7.7× 2.51e-9 2.67e-7 ✓ sig.
Breast cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, MYC, EGF, FZD4, FGF1, AXIN2
 KEGG 19 / 148 5.3× 2.67e-9 2.83e-7 ✓ sig.
MAPK signaling pathway
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, MYC, CHUK, EGF
 KEGG 27 / 299 3.7× 3.50e-9 3.63e-7 ✓ sig.
Phospholipase C-mediated cascade; FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 18 18.4× 3.72e-9 3.85e-7 ✓ sig.
RAF/MAP kinase cascade
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, DLG1, EGF, PDGFRA
 Reactome 17 / 124 5.7× 6.82e-9 6.59e-7 ✓ sig.
Negative regulation of FGFR2 signaling
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, UBB, FGF1
 Reactome 9 / 27 13.8× 7.89e-9 7.46e-7 ✓ sig.
PI3K Cascade
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGF1
 Reactome 10 / 39 10.6× 1.98e-8 1.67e-6 ✓ sig.
FGFR2b ligand binding and activation
FGF10, FGF2, FGF3, FGF7, FGFR2, FGF1
 Reactome 6 / 10 24.8× 3.65e-8 2.87e-6 ✓ sig.
PI-3K cascade:FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 23 14.4× 3.76e-8 2.93e-6 ✓ sig.
SHC-mediated cascade:FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 23 14.4× 3.76e-8 2.93e-6 ✓ 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 ⇵
odontogenesis of dentin-containing tooth
FGF10, TP63, MSX1, PDGFRA, TGFB1, BMP4, BMP2, CTNNA1, GLI2, GLI3, RUNX2, EDA
 GO:0042475 17 / 56 19.6× 6.25e-18 7.20e-15 ✓ sig.
skeletal system development
FGFR1, FGFR3, TP63, COL11A2, COL2A1, TGFB2, BMP4, NOG, ALX4, BMP2, FBN1, GLI2
 GO:0001501 24 / 151 10.2× 1.16e-17 1.30e-14 ✓ sig.
embryonic limb morphogenesis
FGF9, FGFR1, PTCH1, TP63, MSX1, TGFB2, BMP4, TWIST1, CYP26B1, FBN2, GLI3, MEGF8
 GO:0030326 17 / 59 18.6× 1.70e-17 1.84e-14 ✓ sig.
stem cell proliferation
FGF10, FGF2, FGF8, FGF9, FGFR1, IRF6, PTCH1, TP63, RARG, TGFB1, AXIN2, GLI3
 GO:0072089 16 / 54 19.1× 9.29e-17 8.86e-14 ✓ sig.
roof of mouth development
IRF6, SUMO1, BNC2, COL11A2, COL2A1, MSX1, PDGFRA, SATB2, ARID5B, ALX4, DHRS3, GLI3
 GO:0060021 17 / 70 15.6× 4.13e-16 3.57e-13 ✓ sig.
positive regulation of transcription by RNA polymerase II
FGF10, FGF2, FGFR2, IRF6, MAFB, MYC, TP63, GRHL3, CASK, CBFB, CHUK, FZD4
 GO:0045944 59 / 1,208 3.1× 2.09e-15 1.57e-12 ✓ sig.
negative regulation of transcription by RNA polymerase II
FGF9, FGFR1, FGFR2, MAFB, MYC, PTCH1, SUMO1, TP63, CBFB, DLG1, MEIS2, MNT
 GO:0000122 53 / 1,002 3.4× 2.86e-15 2.10e-12 ✓ sig.
positive regulation of cell population proliferation
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, MYC, TP63, DLG1
 GO:0008284 38 / 532 4.6× 3.73e-15 2.69e-12 ✓ sig.
positive regulation of gene expression
FGF2, FGF8, FGF9, MYC, NOS3, SPRY2, GRHL3, EGF, RARG, TGFB1, TGFB2, BMP4
 GO:0010628 37 / 504 4.7× 3.76e-15 2.70e-12 ✓ sig.
lung development
FGF10, FGF2, FGF7, FGF8, FGF9, FGFR1, FGFR2, NOS3, SPRY2, PDGFRA, SIM2, BMP4
 GO:0030324 19 / 108 11.3× 4.47e-15 3.15e-12 ✓ sig.
cell population proliferation
FGF10, FGF2, FGF8, FGF9, FGFR1, FGFR3, IRF6, MYC, DLG1, EGF, FZD4, RARG
 GO:0008283 27 / 263 6.6× 8.18e-15 5.51e-12 ✓ sig.
embryonic cranial skeleton morphogenesis
FGFR2, PDGFRA, BMP4, TWIST1, PRRX1, RUNX2, TGFBR1, WDR19, IRX5, WNT9B, NIPBL, SMAD2
 GO:0048701 12 / 31 24.9× 1.69e-14 1.07e-11 ✓ sig.
limb development
FGF10, IRF6, RARG, NOG, IFT122, GLI3, MEGF8, NPR2, DKK1, GREM1, RARA, VPS54
 GO:0060173 13 / 56 15.0× 2.41e-12 1.03e-9 ✓ sig.
skeletal system morphogenesis
FGFR1, FGFR2, MYC, COL2A1, PDGFRA, RYK, ARID5B, ALX4, MEGF8, RUNX2, TGFBR1, HYAL2
 GO:0048705 12 / 45 17.2× 2.83e-12 1.20e-9 ✓ sig.
odontogenesis
FGF8, FGFR2, MSX1, TGFB2, TGFB3, BMP4, AXIN2, MSX2, EDA, PAX9, WNT10A
 GO:0042476 11 / 36 19.7× 4.43e-12 1.79e-9 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cleft lip Complete unilateral cleft lip 0.947 36 2.56e-108 3.31e-106 ✓ sig.
Cleft palate Complete unilateral cleft lip 0.406 28 5.44e-64 3.56e-62 ✓ sig.
Cleft lip Cleft palate 0.400 28 2.23e-63 1.45e-61 ✓ sig.
Complete unilateral cleft lip Orofacial cleft 0.072 13 1.35e-17 2.27e-16 ✓ sig.
Cleft lip Orofacial cleft 0.072 13 2.06e-17 3.45e-16 ✓ sig.
Cleft lip and palate Orofacial cleft 0.062 10 2.45e-17 4.06e-16 ✓ sig.
Cleft lip and palate Cleft palate 0.118 8 2.06e-16 3.24e-15 ✓ sig.
Cleft palate Orofacial cleft 0.069 14 7.71e-16 1.16e-14 ✓ sig.
Cleft lip and palate Complete unilateral cleft lip 0.130 6 5.19e-13 6.44e-12 ✓ sig.
Cleft lip Cleft lip and palate 0.128 6 6.19e-13 7.58e-12 ✓ sig.
Complete unilateral cleft lip Craniosynostosis 0.079 7 6.43e-11 6.52e-10 ✓ sig.
Cleft lip Craniosynostosis 0.078 7 7.90e-11 7.96e-10 ✓ sig.
Craniosynostosis Tooth agenesis 0.063 6 9.88e-9 7.93e-8 ✓ sig.
Orofacial cleft Tooth agenesis 0.037 7 1.61e-7 1.09e-6 ✓ sig.
Catifa syndrome Cleft lip and palate 0.063 1 9.74e-4 1.67e-3 ✓ sig.
Tooth agenesis tooth agenesis, selective, 9 0.024 1 2.66e-3 3.60e-3 ✓ sig.
Tooth agenesis tooth agenesis, selective, 3 0.024 1 2.66e-3 3.60e-3 ✓ sig.
oligodontia-cancer predisposition syndrome Tooth agenesis 0.024 1 2.66e-3 3.60e-3 ✓ sig.
Craniosynostosis oligodontia-cancer predisposition syndrome 0.017 1 3.83e-3 4.88e-3 ✓ sig.
Craniosynostosis craniosynostosis and dental anomalies 0.017 1 3.83e-3 4.88e-3 ✓ sig.
Craniosynostosis Weiss-kruszka syndrome 0.017 1 3.83e-3 4.88e-3 ✓ sig.
oligodontia-cancer predisposition syndrome Orofacial cleft 0.006 1 1.01e-2 1.15e-2 ✓ sig.
Orofacial cleft Vertebral hypersegmentation with orofacial anomalies 0.006 1 1.01e-2 1.15e-2 ✓ sig.