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 136

10 diseases · 16 shared-gene connections
10 Diseases
259 Unique genes
0.166 Avg. similarity score
Cleft lip Most-connected disease (5 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 ⇵
Cleft lip 5 5 37
Cleft lip and palate 5 5 15
Complete unilateral cleft lip 5 5 36
Orofacial cleft 5 5 156
Cleft palate 4 4 60
Craniosynostosis 4 4 59
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

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

Gene ⇵ Member diseases ⇵ Linked diseases
MSX1 6 / 10 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 2 more
CDH1 5 / 10 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
FGF10 5 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis and 1 more
FGFR1 5 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis and 1 more
IRF6 5 / 10 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
NECTIN1 5 / 10 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
TP63 5 / 10 Cleft lip, Cleft lip and palate, Cleft palate, Complete unilateral cleft lip and 1 more
BMP4 4 / 10 Cleft lip, Cleft lip and palate, Complete unilateral cleft lip, Orofacial cleft
FGFR2 4 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis
FGFR3 4 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis
NOG 4 / 10 Cleft lip, Complete unilateral cleft lip, Craniosynostosis, Orofacial cleft
PTCH1 4 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip, Craniosynostosis
SUMO1 4 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip, Orofacial cleft
ABCA4 3 / 10 Cleft lip, Complete unilateral cleft lip, Orofacial cleft
ARHGAP29 3 / 10 Cleft lip and palate, Cleft palate, Orofacial cleft
BHMT2 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
DLG1 3 / 10 Cleft lip and palate, Cleft palate, Orofacial cleft
FGF2 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF3 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF7 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF8 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
FGF9 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
GDF6 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
KIF7 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
MAFB 3 / 10 Cleft lip, Complete unilateral cleft lip, Orofacial cleft
MTHFD1 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
MTHFR 3 / 10 Cleft lip, Complete unilateral cleft lip, Orofacial cleft
MTHFS 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
MTR 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
MYC 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
NOS3 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
SDC2 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
SLC19A1 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
SPRY2 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
TYMS 3 / 10 Cleft lip, Cleft palate, Complete unilateral cleft lip
AMOTL1 2 / 10 Cleft lip and palate, Orofacial cleft
AXIN2 2 / 10 Craniosynostosis, Orofacial cleft
COL2A1 2 / 10 Cleft palate, Orofacial cleft
DLX4 2 / 10 Cleft lip and palate, Orofacial cleft
FGF1 2 / 10 Cleft lip, Complete unilateral cleft lip
FLNA 2 / 10 Craniosynostosis, Orofacial cleft
GDF11 2 / 10 Orofacial cleft, Vertebral hypersegmentation with orofacial anomalies
IL11RA 2 / 10 Craniosynostosis, craniosynostosis and dental anomalies
MEIS2 2 / 10 Cleft palate, Orofacial cleft
PDGFRA 2 / 10 Cleft lip and palate, Cleft palate
POMT1 2 / 10 Cleft lip, Complete unilateral cleft lip
RIC1 2 / 10 Catifa syndrome, Cleft lip and palate
RUNX2 2 / 10 Craniosynostosis, Orofacial cleft
RYK 2 / 10 Cleft palate, Orofacial cleft
TBX22 2 / 10 Cleft palate, Orofacial cleft
TCN2 2 / 10 Cleft lip, Complete unilateral cleft lip
ZNF462 2 / 10 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 20 / 150 6.2× 6.77e-11 1.01e-8 ✓ sig.
Pathways in cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, MYC, PTCH1, CHUK
 KEGG 37 / 533 3.2× 2.54e-10 3.33e-8 ✓ sig.
Activated point mutants of FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 17 21.8× 8.63e-10 9.83e-8 ✓ sig.
Phospholipase C-mediated cascade; FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 18 20.6× 1.53e-9 1.62e-7 ✓ sig.
Negative regulation of FGFR2 signaling
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, UBB, FGF1
 Reactome 9 / 27 15.5× 2.93e-9 2.92e-7 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, EGF, PDGFRA, FGF1
 Reactome 13 / 75 8.0× 6.22e-9 5.78e-7 ✓ sig.
MAPK signaling pathway
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, MYC, CHUK, EGF
 KEGG 25 / 299 3.9× 6.58e-9 6.08e-7 ✓ sig.
PI3K Cascade
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGF1
 Reactome 10 / 39 11.9× 6.71e-9 6.15e-7 ✓ sig.
RAF/MAP kinase cascade
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, DLG1, EGF, PDGFRA
 Reactome 16 / 124 6.0× 9.35e-9 8.22e-7 ✓ sig.
PI-3K cascade:FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 23 16.1× 1.56e-8 1.29e-6 ✓ sig.
SHC-mediated cascade:FGFR2
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR2, FGF1
 Reactome 8 / 23 16.1× 1.56e-8 1.29e-6 ✓ sig.
FGFR2b ligand binding and activation
FGF10, FGF2, FGF3, FGF7, FGFR2, FGF1
 Reactome 6 / 10 27.8× 1.85e-8 1.50e-6 ✓ sig.
Breast cancer
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, MYC, EGF, FZD4, FGF1, AXIN2
 KEGG 17 / 148 5.3× 1.90e-8 1.53e-6 ✓ sig.
Phospholipase C-mediated cascade: FGFR1
FGF10, FGF2, FGF3, FGF8, FGF9, FGFR1, FGF1
 Reactome 7 / 16 20.3× 1.94e-8 1.56e-6 ✓ sig.
FGFR1b ligand binding and activation
FGF10, FGF2, FGF3, FGFR1, FGF1
 Reactome 5 / 6 38.6× 2.65e-8 2.06e-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 ⇵
stem cell proliferation
FGF10, FGF2, FGF8, FGF9, FGFR1, IRF6, PTCH1, TP63, RARG, TGFB1, AXIN2, GLI3
 GO:0072089 16 / 54 21.4× 1.54e-17 1.73e-14 ✓ sig.
roof of mouth development
IRF6, SUMO1, BNC2, COL11A2, COL2A1, MSX1, PDGFRA, SATB2, ARID5B, ALX4, DHRS3, GLI3
 GO:0060021 17 / 70 17.5× 6.21e-17 6.22e-14 ✓ sig.
embryonic limb morphogenesis
FGF9, FGFR1, PTCH1, TP63, MSX1, TGFB2, BMP4, TWIST1, CYP26B1, FBN2, GLI3, MEGF8
 GO:0030326 16 / 59 19.6× 7.51e-17 7.40e-14 ✓ sig.
skeletal system development
FGFR1, FGFR3, TP63, COL11A2, COL2A1, TGFB2, BMP4, NOG, ALX4, BMP2, FBN1, GLI2
 GO:0001501 22 / 151 10.5× 1.69e-16 1.52e-13 ✓ sig.
positive regulation of cell population proliferation
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, MYC, TP63, DLG1
 GO:0008284 37 / 532 5.0× 5.22e-16 4.31e-13 ✓ sig.
odontogenesis of dentin-containing tooth
FGF10, TP63, MSX1, PDGFRA, TGFB1, BMP4, BMP2, CTNNA1, GLI2, GLI3, RUNX2, BCL11B
 GO:0042475 15 / 56 19.3× 8.73e-16 6.88e-13 ✓ sig.
negative regulation of transcription by RNA polymerase II
FGF9, FGFR1, FGFR2, MAFB, MYC, PTCH1, SUMO1, TP63, CBFB, DLG1, MEIS2, MNT
 GO:0000122 50 / 1,002 3.6× 1.82e-15 1.36e-12 ✓ sig.
positive regulation of transcription by RNA polymerase II
FGF10, FGF2, FGFR2, IRF6, MAFB, MYC, TP63, GRHL3, CASK, CBFB, CHUK, FZD4
 GO:0045944 54 / 1,208 3.2× 1.12e-14 7.24e-12 ✓ sig.
cell population proliferation
FGF10, FGF2, FGF8, FGF9, FGFR1, FGFR3, IRF6, MYC, DLG1, EGF, FZD4, RARG
 GO:0008283 25 / 263 6.9× 3.71e-14 2.20e-11 ✓ sig.
lung development
FGF10, FGF2, FGF7, FGF8, FGF9, FGFR1, FGFR2, NOS3, SPRY2, PDGFRA, SIM2, BMP4
 GO:0030324 17 / 108 11.4× 1.36e-13 7.29e-11 ✓ sig.
skeletal system morphogenesis
FGFR1, FGFR2, MYC, COL2A1, PDGFRA, RYK, ARID5B, ALX4, MEGF8, RUNX2, TGFBR1, HYAL2
 GO:0048705 12 / 45 19.2× 7.47e-13 3.51e-10 ✓ sig.
cartilage development
FGFR3, COL11A2, COL2A1, MSX1, SATB2, BMP4, NOG, BMP2, MSX2, NPR2, PRRX1, BMP6
 GO:0051216 15 / 89 12.2× 1.36e-12 6.10e-10 ✓ sig.
fibroblast growth factor receptor signaling pathway
FGF10, FGF2, FGF3, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, SPRY2, NDST1, FGF1
 GO:0008543 13 / 60 15.6× 1.49e-12 6.58e-10 ✓ sig.
positive regulation of DNA-templated transcription
FGF10, FGF7, IRF6, MAFB, MYC, PTCH1, TP63, GRHL3, EGF, FZD4, GDF6, TBX22
 GO:0045893 39 / 778 3.6× 3.02e-12 1.25e-9 ✓ sig.
positive regulation of stem cell proliferation
FGF10, FGF2, FGF8, FGF9, FGFR1, TP63, TGFB1, GJA1, PRRX1, RUNX2, SOX11
 GO:2000648 11 / 41 19.4× 6.42e-12 2.47e-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 3.50e-106 ✓ sig.
Cleft palate Complete unilateral cleft lip 0.406 28 5.44e-64 3.77e-62 ✓ sig.
Cleft lip Cleft palate 0.400 28 2.23e-63 1.53e-61 ✓ sig.
Complete unilateral cleft lip Orofacial cleft 0.072 13 1.35e-17 2.40e-16 ✓ sig.
Cleft lip Orofacial cleft 0.072 13 2.06e-17 3.64e-16 ✓ sig.
Cleft lip and palate Orofacial cleft 0.062 10 2.45e-17 4.28e-16 ✓ sig.
Cleft lip and palate Cleft palate 0.118 8 2.06e-16 3.43e-15 ✓ sig.
Cleft palate Orofacial cleft 0.069 14 7.71e-16 1.23e-14 ✓ sig.
Cleft lip and palate Complete unilateral cleft lip 0.130 6 5.19e-13 6.82e-12 ✓ sig.
Cleft lip Cleft lip and palate 0.128 6 6.19e-13 8.03e-12 ✓ sig.
Complete unilateral cleft lip Craniosynostosis 0.079 7 6.43e-11 6.90e-10 ✓ sig.
Cleft lip Craniosynostosis 0.078 7 7.90e-11 8.43e-10 ✓ sig.
Catifa syndrome Cleft lip and palate 0.063 1 9.74e-4 1.64e-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.
Orofacial cleft Vertebral hypersegmentation with orofacial anomalies 0.006 1 1.01e-2 1.15e-2 ✓ sig.