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 65

14 diseases · 29 shared-gene connections
14 Diseases
35 Unique genes
0.235 Avg. similarity score
Capillary malformation Most-connected disease (6 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 ⇵
Capillary malformation 6 6 3
Capillary malformation-arteriovenous malformation 6 6 8
Klippel-trenaunay syndrome 6 6 7
Anastomosing haemangioma 5 5 3
Congenital hemangioma 5 5 2
Hereditary hemorrhagic telangiectasia 5 5 7
Parkes weber syndrome 5 5 3
Port-wine stain 5 5 2
Cutis marmorata telangiectatica congenita 4 4 2
Arteriovenous malformations 3 3 2
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 3 3 3
Hydrops fetalis 3 3 16
Cerebrofacial arteriovenous metameric syndrome 1 1 1
telangiectasia, hereditary hemorrhagic, type 5 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RASA1 7 / 14 Arteriovenous malformations, Capillary malformation-arteriovenous malformation, Hereditary hemorrhagic telangiectasia, Hydrops fetalis and 3 more
GNAQ 6 / 14 Anastomosing haemangioma, Capillary malformation, Capillary malformation-arteriovenous malformation, Congenital hemangioma and 2 more
CCNH 5 / 14 Capillary malformation-arteriovenous malformation, Hereditary hemorrhagic telangiectasia, Hydrops fetalis, Klippel-trenaunay syndrome and 1 more
GNA11 5 / 14 Anastomosing haemangioma, Capillary malformation, Congenital hemangioma, Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi and 1 more
PIK3CA 4 / 14 Capillary malformation, Capillary malformation-arteriovenous malformation, Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi, Klippel-trenaunay syndrome
GDF2 2 / 14 Hereditary hemorrhagic telangiectasia, telangiectasia, hereditary hemorrhagic, type 5
GNA14 2 / 14 Anastomosing haemangioma, Cerebrofacial arteriovenous metameric syndrome
KRAS 2 / 14 Arteriovenous malformations, Capillary malformation-arteriovenous malformation
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 ⇵
GnRH secretion
GNA11, GNAQ, KRAS, PIK3CA, PIK3R1, MAP2K1
 KEGG 6 / 65 31.7× 2.85e-8 2.20e-6 ✓ sig.
Long-term depression
GNA11, GNAQ, KRAS, RYR1, MAP2K1
 KEGG 5 / 60 28.6× 7.60e-7 3.84e-5 ✓ sig.
Cholinergic synapse
GNA11, GNAQ, KRAS, PIK3CA, PIK3R1, MAP2K1
 KEGG 6 / 115 17.9× 8.75e-7 4.34e-5 ✓ sig.
Growth hormone synthesis, secretion and action
GNA11, GNAQ, KRAS, PIK3CA, PIK3R1, MAP2K1
 KEGG 6 / 122 16.9× 1.24e-6 5.89e-5 ✓ sig.
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion
GNA11, GNA14, GNAQ
 Reactome 3 / 8 129× 1.26e-6 5.96e-5 ✓ sig.
Downstream signal transduction
RASA1, KRAS, PIK3CA, PIK3R1
 Reactome 4 / 29 47.3× 1.36e-6 6.39e-5 ✓ sig.
Acetylcholine regulates insulin secretion
GNA11, GNA14, GNAQ
 Reactome 3 / 9 114× 1.88e-6 8.34e-5 ✓ sig.
Signaling by FGFR1 in disease
KRAS, PIK3CA, PIK3R1, MYO18A
 Reactome 4 / 33 41.6× 2.33e-6 1.00e-4 ✓ sig.
Pancreatic cancer
KRAS, PIK3CA, PIK3R1, SMAD4, MAP2K1
 KEGG 5 / 77 22.3× 2.65e-6 1.12e-4 ✓ sig.
Chronic myeloid leukemia
KRAS, PIK3CA, PIK3R1, SMAD4, MAP2K1
 KEGG 5 / 77 22.3× 2.65e-6 1.12e-4 ✓ sig.
Signaling by FGFR3 fusions in cancer
KRAS, PIK3CA, PIK3R1
 Reactome 3 / 10 103× 2.68e-6 1.13e-4 ✓ sig.
Apelin signaling pathway
GNAQ, KRAS, SMAD4, RYR1, RYR3, MAP2K1
 KEGG 6 / 140 14.7× 2.77e-6 1.16e-4 ✓ sig.
Signaling pathways regulating pluripotency of stem cells
KRAS, PIK3CA, PIK3R1, SMAD4, DLX5, MAP2K1
 KEGG 6 / 144 14.3× 3.26e-6 1.33e-4 ✓ sig.
Signaling by FGFR4 in disease
KRAS, PIK3CA, PIK3R1
 Reactome 3 / 11 93.6× 3.68e-6 1.48e-4 ✓ sig.
Colorectal cancer
KRAS, PIK3CA, PIK3R1, SMAD4, MAP2K1
 KEGG 5 / 87 19.7× 4.86e-6 1.86e-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 ⇵
angiogenesis
RASA1, PIK3CA, EPHB4, ACVRL1, ENG, GDF2, CCBE1, AGGF1
 GO:0001525 8 / 284 15.0× 4.25e-8 5.91e-6 ✓ sig.
BMP signaling pathway
ACVRL1, ENG, GDF2, SMAD4, DLX5
 GO:0030509 5 / 88 30.3× 6.00e-7 5.45e-5 ✓ sig.
positive regulation of SMAD protein signal transduction
ACVRL1, ENG, GDF2, SMAD4
 GO:0060391 4 / 42 50.8× 1.10e-6 8.93e-5 ✓ sig.
vasculogenesis
RASA1, ENG, GDF2, AGGF1
 GO:0001570 4 / 63 33.9× 5.68e-6 3.32e-4 ✓ sig.
activin receptor signaling pathway
ACVRL1, GDF2, SMAD4
 GO:0032924 3 / 22 72.8× 9.05e-6 4.83e-4 ✓ sig.
endocardial cushion to mesenchymal transition
ACVRL1, ENG
 GO:0090500 2 / 3 356× 1.02e-5 5.30e-4 ✓ sig.
positive regulation of angiogenesis
ACVRL1, ENG, GDF2, CCBE1, AGGF1
 GO:0045766 5 / 159 16.8× 1.11e-5 5.63e-4 ✓ sig.
cellular response to BMP stimulus
ACVRL1, GDF2, SMAD4
 GO:0071773 3 / 33 48.5× 3.16e-5 1.27e-3 ✓ sig.
insulin-like growth factor receptor signaling pathway
PIK3CA, PIK3R1, MAP2K1
 GO:0048009 3 / 33 48.5× 3.16e-5 1.27e-3 ✓ sig.
blood vessel morphogenesis
RASA1, ACVRL1, GDF2
 GO:0048514 3 / 34 47.1× 3.46e-5 1.36e-3 ✓ sig.
positive regulation of gene expression
KRAS, GDF2, SMAD4, FOXP3, DLX5, MAP2K1, PSEN1
 GO:0010628 7 / 504 7.4× 3.48e-5 1.37e-3 ✓ sig.
negative regulation of gene expression
PIK3CA, ACVRL1, ENG, FOXP3, MAP2K1, PSEN1
 GO:0010629 6 / 339 9.4× 3.55e-5 1.39e-3 ✓ sig.
negative regulation of endothelial cell proliferation
ACVRL1, ENG, GDF2
 GO:0001937 3 / 39 41.1× 5.25e-5 1.87e-3 ✓ sig.
positive regulation of BMP signaling pathway
ACVRL1, ENG, GDF2
 GO:0030513 3 / 40 40.0× 5.67e-5 1.97e-3 ✓ sig.
venous blood vessel morphogenesis
ENG, CCBE1
 GO:0048845 2 / 7 153× 7.11e-5 2.35e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Capillary malformation-arteriovenous malformation Klippel-trenaunay syndrome 0.333 4 1.05e-12 1.34e-11 ✓ sig.
Anastomosing haemangioma Congenital hemangioma 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Capillary malformation Congenital hemangioma 0.500 2 2.53e-8 2.03e-7 ✓ sig.
Anastomosing haemangioma Capillary malformation 0.400 2 7.59e-8 5.72e-7 ✓ sig.
Capillary malformation Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0.400 2 7.59e-8 5.72e-7 ✓ sig.
Klippel-trenaunay syndrome Port-wine stain 0.250 2 1.77e-7 1.25e-6 ✓ sig.
Capillary malformation-arteriovenous malformation Port-wine stain 0.222 2 2.36e-7 1.64e-6 ✓ sig.
Arteriovenous malformations Capillary malformation-arteriovenous malformation 0.222 2 2.36e-7 1.64e-6 ✓ sig.
Capillary malformation Klippel-trenaunay syndrome 0.222 2 5.31e-7 3.46e-6 ✓ sig.
Klippel-trenaunay syndrome Parkes weber syndrome 0.222 2 5.31e-7 3.46e-6 ✓ sig.
Hereditary hemorrhagic telangiectasia Parkes weber syndrome 0.222 2 5.31e-7 3.46e-6 ✓ sig.
Capillary malformation Capillary malformation-arteriovenous malformation 0.200 2 7.08e-7 4.51e-6 ✓ sig.
Capillary malformation-arteriovenous malformation Parkes weber syndrome 0.200 2 7.08e-7 4.51e-6 ✓ sig.
Hydrops fetalis Parkes weber syndrome 0.111 2 3.04e-6 1.72e-5 ✓ sig.
Hereditary hemorrhagic telangiectasia Klippel-trenaunay syndrome 0.154 2 3.72e-6 2.09e-5 ✓ sig.
Capillary malformation-arteriovenous malformation Hereditary hemorrhagic telangiectasia 0.143 2 4.95e-6 2.72e-5 ✓ sig.
Hydrops fetalis Klippel-trenaunay syndrome 0.091 2 2.12e-5 1.06e-4 ✓ sig.
Hereditary hemorrhagic telangiectasia Hydrops fetalis 0.091 2 2.12e-5 1.06e-4 ✓ sig.
Anastomosing haemangioma Cerebrofacial arteriovenous metameric syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital hemangioma Port-wine stain 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Congenital hemangioma Cutis marmorata telangiectatica congenita 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Arteriovenous malformations Port-wine stain 0.250 1 2.60e-4 6.40e-4 ✓ sig.
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi Cutis marmorata telangiectatica congenita 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Capillary malformation Cutis marmorata telangiectatica congenita 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Congenital hemangioma Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Anastomosing haemangioma Port-wine stain 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Anastomosing haemangioma Cutis marmorata telangiectatica congenita 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Arteriovenous malformations Parkes weber syndrome 0.200 1 3.90e-4 8.52e-4 ✓ sig.
Hereditary hemorrhagic telangiectasia telangiectasia, hereditary hemorrhagic, type 5 0.125 1 4.55e-4 9.55e-4 ✓ sig.