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 221

9 diseases · 14 shared-gene connections
9 Diseases
28 Unique genes
0.224 Avg. similarity score
Epistaxis Most-connected disease (6 links)
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Disease Searched: Palate telangiectasia 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 ⇵
Epistaxis 6 6 2
Cerebral arteriovenous malformations 5 5 23
Intracranial arteriovenous malformation 4 4 3
Hereditary hemorrhagic telangiectasia 3 3 7
Lip telangiectasia 3 3 1
Palate telangiectasia 3 3 1
Telangiectasia 2 2 1
Cerebellar vermis atrophy 1 1 1
Neurodevelopmental disorder with microcephaly, ataxia, and seizures 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ENG 6 / 9 Cerebral arteriovenous malformations, Epistaxis, Hereditary hemorrhagic telangiectasia, Intracranial arteriovenous malformation and 2 more
ACVRL1 4 / 9 Cerebral arteriovenous malformations, Epistaxis, Hereditary hemorrhagic telangiectasia, Telangiectasia
IL6 2 / 9 Cerebral arteriovenous malformations, Intracranial arteriovenous malformation
KRAS 2 / 9 Cerebral arteriovenous malformations, Intracranial arteriovenous malformation
SARS1 2 / 9 Cerebral arteriovenous malformations, Neurodevelopmental disorder with microcephaly, ataxia, and seizures
SYN3 2 / 9 Cerebellar vermis atrophy, Cerebral arteriovenous malformations
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 ⇵
Signaling by BMP
ZFYVE16, ACVRL1, GDF2, SMAD4
 Reactome 4 / 28 61.3× 4.66e-7 2.15e-5 ✓ sig.
FoxO signaling pathway
BRAF, EGFR, KRAS, IL6, SMAD4
 KEGG 5 / 133 16.1× 1.24e-5 3.47e-4 ✓ sig.
Pancreatic cancer
BRAF, EGFR, KRAS, SMAD4
 KEGG 4 / 77 22.3× 2.85e-5 6.94e-4 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
BRAF, EGFR, KRAS, IL6
 KEGG 4 / 80 21.4× 3.31e-5 7.86e-4 ✓ sig.
Colorectal cancer
BRAF, EGFR, KRAS, SMAD4
 KEGG 4 / 87 19.7× 4.61e-5 1.02e-3 ✓ sig.
MAPK signaling pathway
BRAF, CACNA1H, EGFR, KRAS, MAP4K4, RASA1
 KEGG 6 / 299 8.6× 5.37e-5 1.15e-3 ✓ sig.
Endocrine resistance
BRAF, EGFR, KRAS, NOTCH4
 KEGG 4 / 99 17.3× 7.64e-5 1.53e-3 ✓ sig.
MAP2K and MAPK activation
BRAF, IL17RD, KRAS
 Reactome 3 / 40 32.2× 1.06e-4 1.98e-3 ✓ sig.
Bladder cancer
BRAF, EGFR, KRAS
 KEGG 3 / 41 31.4× 1.14e-4 2.10e-3 ✓ sig.
Pathways in cancer
BRAF, EGFR, GLI2, KRAS, NOTCH4, IL6, SMAD4
 KEGG 7 / 533 5.6× 1.71e-4 2.91e-3 ✓ sig.
EGFR Transactivation by Gastrin
EGFR, KRAS
 Reactome 2 / 9 95.3× 1.87e-4 3.11e-3 ✓ sig.
Endometrial cancer
BRAF, EGFR, KRAS
 KEGG 3 / 59 21.8× 3.38e-4 4.94e-3 ✓ sig.
Breast cancer
BRAF, EGFR, KRAS, NOTCH4
 KEGG 4 / 148 11.6× 3.60e-4 5.18e-3 ✓ sig.
Gastric cancer
BRAF, EGFR, KRAS, SMAD4
 KEGG 4 / 150 11.4× 3.79e-4 5.39e-3 ✓ sig.
GRB2 events in EGFR signaling
EGFR, KRAS
 Reactome 2 / 13 66.0× 4.02e-4 5.65e-3 ✓ 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 ⇵
positive regulation of peptidyl-serine phosphorylation
BRAF, EGFR, PDCD10, IL6
 GO:0033138 4 / 20 133× 1.92e-8 3.11e-6 ✓ sig.
blood vessel morphogenesis
CDH2, ACVRL1, GDF2, RASA1
 GO:0048514 4 / 34 78.5× 1.81e-7 2.08e-5 ✓ sig.
positive regulation of SMAD protein signal transduction
ENG, ACVRL1, GDF2, SMAD4
 GO:0060391 4 / 42 63.6× 4.34e-7 4.32e-5 ✓ sig.
activin receptor signaling pathway
ACVRL1, GDF2, SMAD4
 GO:0032924 3 / 22 91.0× 4.55e-6 2.94e-4 ✓ sig.
endocardial cushion to mesenchymal transition
ENG, ACVRL1
 GO:0090500 2 / 3 445× 6.49e-6 3.90e-4 ✓ sig.
positive regulation of gene expression
BRAF, KRAS, PDCD10, IL6, GDF2, SMAD4, PSEN1
 GO:0010628 7 / 504 9.3× 7.21e-6 4.22e-4 ✓ sig.
BMP signaling pathway
ENG, ACVRL1, GDF2, SMAD4
 GO:0030509 4 / 88 30.3× 8.62e-6 4.85e-4 ✓ sig.
negative regulation of apoptotic process
BRAF, EGFR, MAP4K4, PDCD10, IL6, RASA1, PSEN1
 GO:0043066 7 / 524 8.9× 9.29e-6 5.14e-4 ✓ sig.
cellular response to BMP stimulus
ACVRL1, GDF2, SMAD4
 GO:0071773 3 / 33 60.7× 1.59e-5 7.80e-4 ✓ sig.
branching involved in blood vessel morphogenesis
ENG, NOTCH4, GDF2
 GO:0001569 3 / 33 60.7× 1.59e-5 7.80e-4 ✓ sig.
negative regulation of endothelial cell proliferation
ENG, ACVRL1, GDF2
 GO:0001937 3 / 39 51.3× 2.66e-5 1.14e-3 ✓ sig.
positive regulation of BMP signaling pathway
ENG, ACVRL1, GDF2
 GO:0030513 3 / 40 50.1× 2.87e-5 1.21e-3 ✓ sig.
positive regulation of transcription by RNA polymerase II
EGFR, ENG, GLI2, NLRP3, NOTCH4, IL6, ACVRL1, GDF2, SMAD4
 GO:0045944 9 / 1,208 5.0× 4.30e-5 1.64e-3 ✓ sig.
negative regulation of endothelial cell differentiation
NOTCH4, ACVRL1
 GO:0045602 2 / 7 191× 4.53e-5 1.71e-3 ✓ sig.
positive regulation of Notch signaling pathway
PDCD10, ACVRL1, GDF2
 GO:0045747 3 / 50 40.0× 5.63e-5 2.01e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Epistaxis Hereditary hemorrhagic telangiectasia 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Cerebral arteriovenous malformations Intracranial arteriovenous malformation 0.091 2 1.75e-6 1.03e-5 ✓ sig.
Cerebral arteriovenous malformations Epistaxis 0.091 2 1.75e-6 1.03e-5 ✓ sig.
Cerebral arteriovenous malformations Hereditary hemorrhagic telangiectasia 0.074 2 3.66e-5 1.88e-4 ✓ sig.
Lip telangiectasia Palate telangiectasia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epistaxis Lip telangiectasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epistaxis Palate telangiectasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epistaxis Telangiectasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intracranial arteriovenous malformation Lip telangiectasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Intracranial arteriovenous malformation Palate telangiectasia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Epistaxis Intracranial arteriovenous malformation 0.250 1 2.58e-4 5.38e-4 ✓ sig.
Hereditary hemorrhagic telangiectasia Telangiectasia 0.125 1 4.52e-4 8.26e-4 ✓ sig.
Cerebellar vermis atrophy Cerebral arteriovenous malformations 0.045 1 1.36e-3 1.97e-3 ✓ sig.
Cerebral arteriovenous malformations Neurodevelopmental disorder with microcephaly, ataxia, and seizures 0.045 1 1.36e-3 1.97e-3 ✓ sig.