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 112

10 diseases · 14 shared-gene connections
10 Diseases
456 Unique genes
0.060 Avg. similarity score
Congenital heart disease Most-connected disease (6 links)
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Disease Searched: Craniofacial abnormalities 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 ⇵
Congenital heart disease 6 6 172
Tetralogy of fallot 6 6 114
Congenital heart defects 5 5 70
Chromosome 15q deletion syndrome 2 2 1
Conotruncal cardiac defect 2 2 63
Craniofacial abnormalities 2 2 156
Hypoplastic left heart syndrome 2 2 18
El-hayek-chahrour neurodevelopmental syndrome 1 1 1
Truncus arteriosus 1 1 1
White-kernohan syndrome 1 1 1

Top shared genes (genes linked to 2+ member diseases ‐ top 100 shown, download for all)

Gene ⇵ Member diseases ⇵ Linked diseases
TBX1 6 / 10 Congenital heart defects, Congenital heart disease, Conotruncal cardiac defect, Craniofacial abnormalities and 2 more
AHR 4 / 10 Congenital heart defects, Congenital heart disease, Conotruncal cardiac defect, Craniofacial abnormalities
GDF1 4 / 10 Congenital heart defects, Congenital heart disease, Conotruncal cardiac defect, Tetralogy of fallot
MYH7 4 / 10 Congenital heart defects, Congenital heart disease, Hypoplastic left heart syndrome, Tetralogy of fallot
NIPBL 4 / 10 Congenital heart defects, Congenital heart disease, Craniofacial abnormalities, Tetralogy of fallot
NKX2-5 4 / 10 Congenital heart disease, Conotruncal cardiac defect, Hypoplastic left heart syndrome, Tetralogy of fallot
NOTCH1 4 / 10 Congenital heart disease, Craniofacial abnormalities, Hypoplastic left heart syndrome, Tetralogy of fallot
ABL1 3 / 10 Congenital heart defects, Congenital heart disease, Tetralogy of fallot
CERS1 3 / 10 Congenital heart defects, Congenital heart disease, Tetralogy of fallot
CRIPTO 3 / 10 Congenital heart defects, Congenital heart disease, Tetralogy of fallot
FOXH1 3 / 10 congenital heart disease, Conotruncal cardiac defect, Tetralogy of fallot
FOXP1 3 / 10 Congenital heart defects, Congenital heart disease, Hypoplastic left heart syndrome
FOXP2 3 / 10 Congenital heart disease, Conotruncal cardiac defect, Craniofacial abnormalities
GATA4 3 / 10 Congenital heart defects, Congenital heart disease, Tetralogy of fallot
GATA6 3 / 10 Congenital heart defects, Conotruncal cardiac defect, Tetralogy of fallot
HAND1 3 / 10 Congenital heart disease, Hypoplastic left heart syndrome, Tetralogy of fallot
HAND2 3 / 10 Congenital heart defects, Congenital heart disease, Tetralogy of fallot
LEFTY2 3 / 10 Congenital heart defects, Congenital heart disease, Tetralogy of fallot
MCTP2 3 / 10 Chromosome 15q deletion syndrome, Congenital heart disease, Tetralogy of fallot
MYH6 3 / 10 Congenital heart defects, Hypoplastic left heart syndrome, Tetralogy of fallot
NKX2-6 3 / 10 Congenital heart disease, Conotruncal cardiac defect, Tetralogy of fallot
PITX2 3 / 10 Congenital heart defects, Congenital heart disease, Craniofacial abnormalities
RBFOX2 3 / 10 Congenital heart disease, Hypoplastic left heart syndrome, Tetralogy of fallot
RCAN1 3 / 10 Congenital heart defects, Congenital heart disease, Craniofacial abnormalities
STRA6 3 / 10 Congenital heart defects, Congenital heart disease, Craniofacial abnormalities
TBX20 3 / 10 Congenital heart disease, Hypoplastic left heart syndrome, Tetralogy of fallot
TGFB2 3 / 10 Congenital heart defects, Congenital heart disease, Craniofacial abnormalities
UFD1 3 / 10 Congenital heart defects, Congenital heart disease, Craniofacial abnormalities
ZIC3 3 / 10 Congenital heart disease, Craniofacial abnormalities, Tetralogy of fallot
ADAM29 2 / 10 Congenital heart disease, Conotruncal cardiac defect
ADAMTS19 2 / 10 Congenital heart defects, Congenital heart disease
ANKRD1 2 / 10 Congenital heart disease, Tetralogy of fallot
ANKRD11 2 / 10 Congenital heart disease, Tetralogy of fallot
BMPR1A 2 / 10 Congenital heart disease, Craniofacial abnormalities
CARTPT 2 / 10 Congenital heart disease, Conotruncal cardiac defect
CDH13 2 / 10 Congenital heart disease, Conotruncal cardiac defect
CDK13 2 / 10 Congenital heart defects, Congenital heart disease
CFAP53 2 / 10 Hypoplastic left heart syndrome, Tetralogy of fallot
CITED2 2 / 10 Congenital heart disease, Tetralogy of fallot
COL11A2 2 / 10 Congenital heart defects, Craniofacial abnormalities
COL2A1 2 / 10 Congenital heart defects, Craniofacial abnormalities
CRELD1 2 / 10 Congenital heart disease, Tetralogy of fallot
CTSG 2 / 10 Congenital heart disease, Conotruncal cardiac defect
DCHS1 2 / 10 Congenital heart disease, Tetralogy of fallot
DDB1 2 / 10 Congenital heart defects, White-kernohan syndrome
ECE1 2 / 10 Congenital heart defects, Craniofacial abnormalities
EDN1 2 / 10 Congenital heart defects, Craniofacial abnormalities
EDNRA 2 / 10 Congenital heart defects, Craniofacial abnormalities
ETV2 2 / 10 Congenital heart defects, Hypoplastic left heart syndrome
EYA1 2 / 10 Congenital heart defects, Craniofacial abnormalities
FGF8 2 / 10 Congenital heart disease, Craniofacial abnormalities
FLNA 2 / 10 Congenital heart defects, Tetralogy of fallot
FLT4 2 / 10 Congenital heart disease, Tetralogy of fallot
FOLR1 2 / 10 Congenital heart defects, Craniofacial abnormalities
FOXC2 2 / 10 Craniofacial abnormalities, Tetralogy of fallot
FOXL1 2 / 10 Congenital heart disease, Tetralogy of fallot
GATA5 2 / 10 Congenital heart disease, Tetralogy of fallot
GJA1 2 / 10 Congenital heart disease, Hypoplastic left heart syndrome
GJA5 2 / 10 Congenital heart disease, Tetralogy of fallot
GNAQ 2 / 10 Congenital heart defects, Craniofacial abnormalities
GP1BB 2 / 10 Congenital heart defects, Craniofacial abnormalities
HEY2 2 / 10 Congenital heart disease, Tetralogy of fallot
HOXA1 2 / 10 Congenital heart defects, Craniofacial abnormalities
HOXA3 2 / 10 Congenital heart defects, Craniofacial abnormalities
IQCJ 2 / 10 Congenital heart disease, Conotruncal cardiac defect
IQCJ-SCHIP1 2 / 10 Congenital heart disease, Conotruncal cardiac defect
IRX4 2 / 10 Congenital heart disease, Tetralogy of fallot
IRX5 2 / 10 Congenital heart defects, Craniofacial abnormalities
ISL1 2 / 10 Congenital heart defects, Congenital heart disease
JAG1 2 / 10 Congenital heart defects, Tetralogy of fallot
KDM5A 2 / 10 Congenital heart disease, El-hayek-chahrour neurodevelopmental syndrome
LRP2 2 / 10 Congenital heart disease, Craniofacial abnormalities
MAP1B 2 / 10 Congenital heart disease, Conotruncal cardiac defect
MED13L 2 / 10 Congenital heart disease, Tetralogy of fallot
MTHFR 2 / 10 Congenital heart defects, Tetralogy of fallot
MYH11 2 / 10 Congenital heart disease, Tetralogy of fallot
MYRF 2 / 10 Congenital heart defects, Tetralogy of fallot
NFATC1 2 / 10 Congenital heart defects, Congenital heart disease
NONO 2 / 10 Congenital heart disease, Tetralogy of fallot
NPPB 2 / 10 Congenital heart defects, Congenital heart disease
NR2F2 2 / 10 Congenital heart disease, Tetralogy of fallot
NRP1 2 / 10 Congenital heart disease, Tetralogy of fallot
PDGFRA 2 / 10 Congenital heart disease, Craniofacial abnormalities
PLXND1 2 / 10 Congenital heart disease, Tetralogy of fallot
POU5F1 2 / 10 Congenital heart defects, Congenital heart disease
PRKD1 2 / 10 Congenital heart disease, Tetralogy of fallot
PTCH1 2 / 10 Congenital heart disease, Craniofacial abnormalities
ROBO1 2 / 10 Congenital heart disease, Tetralogy of fallot
SCHIP1 2 / 10 Congenital heart disease, Conotruncal cardiac defect
SLC29A3 2 / 10 Congenital heart defects, Congenital heart disease
SMAD2 2 / 10 Congenital heart disease, Craniofacial abnormalities
SMAD6 2 / 10 Congenital heart disease, Tetralogy of fallot
SOX7 2 / 10 Congenital heart disease, Tetralogy of fallot
SRF 2 / 10 Congenital heart disease, Tetralogy of fallot
TAB2 2 / 10 Congenital heart disease, Tetralogy of fallot
TAF1 2 / 10 Congenital heart disease, Tetralogy of fallot
TBX5 2 / 10 Congenital heart disease, Tetralogy of fallot
TFAP2B 2 / 10 Craniofacial abnormalities, Tetralogy of fallot
TLL1 2 / 10 Congenital heart disease, Tetralogy of fallot
TMEM260 2 / 10 Tetralogy of fallot, Truncus arteriosus
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 ⇵
TGF-beta signaling pathway
LEFTY2, MAPK1, PITX2, SMAD6, TGFB2, BMPR1A, BMP7, SMAD2, ACVR1, BMPR2, CHRD, HDAC1
 KEGG 27 / 108 6.6× 2.52e-15 8.18e-13 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
HOXA1, ISL1, KLF4, LEFTY2, MAPK1, POU5F1, BMPR1A, ZIC3, SMAD2, ACVR1, BMPR2, HAND1
 KEGG 28 / 144 5.1× 6.73e-13 1.43e-10 ✓ sig.
Pathways in cancer
ABL1, EDN1, EDNRA, GNA11, GNAQ, GSTM1, GSTP1, GSTT1, HIF1A, JAG1, MAPK1, NOTCH1
 KEGG 56 / 533 2.8× 2.98e-12 5.55e-10 ✓ sig.
Breast cancer
JAG1, MAPK1, NOTCH1, FGF10, FLT4, FGF8, HEY1, HEY2, CSNK1A1, CTNNB1, DLL3, EGFR
 KEGG 23 / 148 4.1× 7.90e-9 6.87e-7 ✓ sig.
Proteoglycans in cancer
CAV3, FLNA, HIF1A, MAPK1, TGFB2, VEGFA, SMAD2, COL1A1, COL1A2, PTCH1, ROCK2, ACTB
 KEGG 27 / 204 3.5× 1.41e-8 1.15e-6 ✓ sig.
Thyroid hormone signaling pathway
GATA4, HIF1A, MAPK1, MYH6, MYH7, NOTCH1, RCAN1, HDAC1, MED13L, RXRA, ACTB, ACTG1
 KEGG 20 / 122 4.3× 3.00e-8 2.25e-6 ✓ sig.
Signaling by BMP
SMAD6, BMPR1A, BMP10, BMPR2, SMAD1, SMAD7, BMPR1B, SKI, SMAD4, ACVR2B
 Reactome 10 / 28 9.4× 4.00e-8 2.90e-6 ✓ sig.
Gastric cancer
MAPK1, TGFB2, FGF10, SMAD2, CTNNA3, FGF8, RXRA, CSNK1A1, CTNNB1, EGFR, FGF3, FGFR2
 KEGG 22 / 150 3.9× 4.93e-8 3.51e-6 ✓ sig.
Cytoskeleton in muscle cells
COL11A2, MYH6, MYH7, XIRP2, ANKRD1, COL1A1, COL1A2, CSRP1, DTNA, FBLN2, MYBPC3, MYH11
 KEGG 27 / 232 3.1× 2.13e-7 1.27e-5 ✓ sig.
Adherens junction
MAPK1, CTNNA3, MYL2, ROCK2, SNAI1, ACTB, ACTG1, CTNNB1, EGFR, EP300, FGFR1, RHOA
 KEGG 16 / 93 4.5× 3.70e-7 2.06e-5 ✓ sig.
Hepatocellular carcinoma
GSTM1, GSTP1, GSTT1, MAPK1, TGFB2, SMAD2, ACTB, ACTG1, CSNK1A1, CTNNB1, EGFR, FZD4
 KEGG 22 / 170 3.4× 4.67e-7 2.52e-5 ✓ sig.
Focal adhesion
CAV3, COL2A1, FLNA, MAPK1, VEGFA, FLT4, COL1A1, COL1A2, CRKL, MYL2, PDGFRA, ROCK2
 KEGG 24 / 203 3.1× 7.60e-7 3.83e-5 ✓ sig.
Chronic myeloid leukemia
ABL1, MAPK1, TGFB2, CRKL, HDAC1, SMAD3, SMAD4, TGFBR2, TP53, BRAF, KRAS, PTPN11
 KEGG 14 / 77 4.8× 9.94e-7 4.85e-5 ✓ sig.
NOTCH4 Intracellular Domain Regulates Transcription
MAML3, NOTCH1, HEY1, HEY2, MAML2, EP300, NOTCH2
 Reactome 7 / 17 10.8× 1.52e-6 6.98e-5 ✓ sig.
Transcriptional regulation of pluripotent stem cells
FOXP1, KLF4, POU5F1, ZIC3, SMAD2, SALL4, SMAD4
 Reactome 7 / 17 10.8× 1.52e-6 6.98e-5 ✓ 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 ⇵
heart development
DYNC2H1, ECE1, EDN1, EDNRA, GATA4, GNA11, HAND2, ISL1, MAPK1, MKKS, NIPBL, NKX2-5
 GO:0007507 70 / 273 10.5× 1.43e-51 3.33e-47 ✓ sig.
positive regulation of transcription by RNA polymerase II
ABL1, AHR, CBFB, CDK13, CDK8, EDN1, ETV2, EYA1, GATA4, GATA6, HAND2, HIF1A
 GO:0045944 121 / 1,208 4.1× 9.36e-43 1.21e-38 ✓ sig.
positive regulation of DNA-templated transcription
AHR, EYA1, GATA4, GATA6, HAND2, HIF1A, KLF4, MYRF, NFATC1, NKX2-5, NOTCH1, PITX2
 GO:0045893 85 / 778 4.5× 3.14e-32 1.89e-28 ✓ sig.
negative regulation of transcription by RNA polymerase II
CBFB, EDN1, FOXP1, GATA4, GATA6, GSTP1, IRX1, ISL1, KLF4, NIPBL, NKX2-5, NOTCH1
 GO:0000122 96 / 1,002 3.9× 7.33e-32 4.26e-28 ✓ sig.
skeletal system development
COL11A2, COL2A1, EDN1, GDF3, GNA11, TGFB2, TLL1, UFD1, ZIC3, BMP7, CHRD, COL1A1
 GO:0001501 41 / 151 11.1× 1.81e-31 1.00e-27 ✓ sig.
outflow tract morphogenesis
EYA1, HAND2, HIF1A, ISL1, NIPBL, NKX2-5, NOTCH1, PITX2, TBX1, TBX20, TGFB2, VEGFA
 GO:0003151 29 / 63 18.9× 2.51e-30 1.23e-26 ✓ sig.
regulation of transcription by RNA polymerase II
AHR, CBFB, ETV2, FOXP1, GATA4, GATA6, HAND2, HIF1A, HOXA1, HOXA3, IRX1, IRX5
 GO:0006357 113 / 1,602 2.9× 8.30e-26 2.79e-22 ✓ sig.
regulation of DNA-templated transcription
ABL1, AHR, ETV2, FOXP1, GATA4, GATA6, HAND2, HIF1A, HOXA1, HOXA3, IRX1, IRX5
 GO:0006355 106 / 1,454 3.0× 2.96e-25 9.31e-22 ✓ sig.
outflow tract septum morphogenesis
GATA6, ISL1, NKX2-5, ROBO1, SMAD6, TBX1, TBX20, TGFB2, BMPR1A, ACVR1, BMPR2, FGF8
 GO:0003148 19 / 28 27.8× 8.94e-25 2.64e-21 ✓ sig.
heart morphogenesis
COL2A1, HAND2, ISL1, NIPBL, NKX2-5, TBX1, TGFB2, VEGFA, BMPR1A, DLC1, DCHS1, FGF8
 GO:0003007 25 / 61 16.8× 9.88e-25 2.90e-21 ✓ sig.
cell differentiation
CAV3, ETV2, EYA1, GATA4, GATA6, HAND2, HIF1A, ISL1, MYRF, NKX2-5, NOTCH1, PRKD1
 GO:0030154 86 / 1,051 3.4× 1.18e-23 3.21e-20 ✓ sig.
lung development
NOTCH1, PITX2, STRA6, TBX5, VEGFA, BMPR1A, FGF10, ZIC3, SMAD2, BMPR2, FGF8, FOXP2
 GO:0030324 30 / 108 11.4× 1.25e-23 3.35e-20 ✓ sig.
roof of mouth development
COL11A2, COL2A1, HAND2, WDPCP, BMPR1A, OSR1, PDGFRA, SNAI1, TCF21, ALX1, ALX4, BNC2
 GO:0060021 24 / 70 14.1× 1.36e-21 2.70e-18 ✓ sig.
positive regulation of gene expression
ETV2, HAND2, HIF1A, IRX1, KLF4, NKX2-5, NOTCH1, PRKD1, ROBO1, TGFB2, VEGFA, BMPR1A
 GO:0010628 55 / 504 4.5× 7.27e-21 1.30e-17 ✓ sig.
ventricular septum morphogenesis
ADAMTS19, NKX2-5, NOTCH1, PITX2, ROBO1, TGFB2, BMPR1A, CITED2, ACVR1, BMPR2, GJA5, HEY1
 GO:0060412 19 / 41 19.0× 2.36e-20 3.99e-17 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital heart disease Tetralogy of fallot 0.186 45 1.96e-59 1.19e-57 ✓ sig.
Congenital heart defects Congenital heart disease 0.120 26 1.85e-33 6.37e-32 ✓ sig.
Congenital heart defects Craniofacial abnormalities 0.097 20 3.90e-24 9.14e-23 ✓ sig.
Congenital heart defects Tetralogy of fallot 0.095 16 4.88e-20 9.35e-19 ✓ sig.
Congenital heart disease Conotruncal cardiac defect 0.068 15 2.17e-16 3.43e-15 ✓ sig.
Hypoplastic left heart syndrome Tetralogy of fallot 0.073 9 2.23e-15 3.26e-14 ✓ sig.
Congenital heart disease Craniofacial abnormalities 0.054 17 1.69e-12 1.98e-11 ✓ sig.
Congenital heart defects Hypoplastic left heart syndrome 0.060 5 1.37e-8 1.09e-7 ✓ sig.
Conotruncal cardiac defect Tetralogy of fallot 0.041 7 3.98e-7 2.51e-6 ✓ sig.
Congenital heart defects White-kernohan syndrome 0.014 1 4.55e-3 5.67e-3 ✓ sig.
Chromosome 15q deletion syndrome Tetralogy of fallot 0.009 1 7.40e-3 8.70e-3 ✓ sig.
Tetralogy of fallot Truncus arteriosus 0.009 1 7.40e-3 8.70e-3 ✓ sig.
Chromosome 15q deletion syndrome Congenital heart disease 0.006 1 1.12e-2 1.26e-2 ✓ sig.
Congenital heart disease El-hayek-chahrour neurodevelopmental syndrome 0.006 1 1.12e-2 1.26e-2 ✓ sig.