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 53

16 diseases · 45 shared-gene connections
16 Diseases
15 Unique genes
0.346 Avg. similarity score
Clapo syndrome Most-connected disease (11 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 ⇵
Clapo syndrome 11 11 1
Cloves syndrome 11 11 1
Congenital intestinal duplication 11 11 1
Congenital macrodactylia 9 9 1
Congenital malformation syndromes involving early overgrowth 9 9 1
Capillary-lymphatic-venous malformation 5 5 2
Congenital hemihypertrophy 5 5 4
Diaphragmatic malformations 5 5 5
Hemifacial myohyperplasia 5 5 1
Hemihyperplasia multiple lipomatosis syndrome 5 5 1
Vascular malformation 5 5 3
Weaver syndrome 5 5 5
Charcot-Marie-Tooth disease type 2A1 1 1 1
Charcot-Marie-Tooth disease type 4C 1 1 1
Cohen-gibson syndrome 1 1 1
Upper extremity deformity, congenital 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PIK3CA 12 / 16 Capillary-lymphatic-venous malformation, Clapo syndrome, Cloves syndrome, Congenital hemihypertrophy and 8 more
EED 2 / 16 Cohen-gibson syndrome, Weaver syndrome
EZH2 2 / 16 Upper extremity deformity, congenital, Weaver syndrome
KIF1B 2 / 16 Charcot-Marie-Tooth disease type 2A1, Congenital hemihypertrophy
SH3TC2 2 / 16 Charcot-Marie-Tooth disease type 4C, Congenital hemihypertrophy
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 ⇵
PKMTs methylate histone lysines
EED, EZH2, NSD1, SUZ12
 Reactome 4 / 71 45.1× 1.46e-6 6.77e-5 ✓ sig.
Transcriptional Regulation by E2F6
EED, EZH2, SUZ12
 Reactome 3 / 35 68.6× 1.01e-5 3.38e-4 ✓ sig.
Regulation of PTEN gene transcription
EED, EZH2, SUZ12
 Reactome 3 / 53 45.3× 3.56e-5 9.62e-4 ✓ sig.
PI3K/AKT activation
PIK3CA, RHOA
 Reactome 2 / 9 178× 5.22e-5 1.32e-3 ✓ sig.
VEGFA-VEGFR2 Pathway
PIK3CA, RHOA, ELMO2
 Reactome 3 / 62 38.7× 5.70e-5 1.42e-3 ✓ sig.
PRC2 methylates histones and DNA
EED, EZH2, SUZ12
 Reactome 3 / 73 32.9× 9.30e-5 2.11e-3 ✓ sig.
Bacterial invasion of epithelial cells
PIK3CA, RHOA, ELMO2
 KEGG 3 / 78 30.8× 1.13e-4 2.48e-3 ✓ sig.
PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases
RHOA, ELMO2
 Reactome 2 / 14 114× 1.31e-4 2.80e-3 ✓ sig.
Polycomb repressive complex
EED, EZH2, SUZ12
 KEGG 3 / 83 28.9× 1.36e-4 2.88e-3 ✓ sig.
EPHA-mediated growth cone collapse
RHOA, YES1
 Reactome 2 / 20 80.1× 2.73e-4 4.98e-3 ✓ sig.
Regulation of signaling by CBL
PIK3CA, YES1
 Reactome 2 / 21 76.3× 3.02e-4 5.39e-3 ✓ sig.
Oxidative Stress Induced Senescence
EED, EZH2, SUZ12
 Reactome 3 / 125 19.2× 4.57e-4 7.43e-3 ✓ sig.
MicroRNAs in cancer
PIK3CA, RHOA, ZFPM2, EZH2
 KEGG 4 / 311 10.3× 4.80e-4 7.72e-3 ✓ sig.
HCMV Early Events
EED, EZH2, SUZ12
 Reactome 3 / 135 17.8× 5.72e-4 8.86e-3 ✓ sig.
Yersinia infection
PIK3CA, RHOA, ELMO2
 KEGG 3 / 138 17.4× 6.10e-4 9.32e-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 ⇵
facultative heterochromatin formation
EED, EZH2, SUZ12
 GO:0140718 3 / 7 534× 1.46e-8 2.38e-6 ✓ sig.
liver development
PIK3CA, ALDH1A2, HLX
 GO:0001889 3 / 87 43.0× 4.26e-5 1.60e-3 ✓ sig.
positive regulation of protein serine/threonine kinase activity
RHOA, EZH2
 GO:0071902 2 / 15 166× 6.28e-5 2.13e-3 ✓ sig.
cardiac muscle tissue development
ZFPM2, ALDH1A2
 GO:0048738 2 / 24 104× 1.64e-4 4.39e-3 ✓ sig.
chromatin organization
EED, EZH2, NSD1, SUZ12
 GO:0006325 4 / 449 11.1× 3.64e-4 7.65e-3 ✓ sig.
oligodendrocyte differentiation
EED, SUZ12
 GO:0048709 2 / 45 55.4× 5.84e-4 1.06e-2 ✓ sig.
endothelial cell migration
PIK3CA, RHOA
 GO:0043542 2 / 48 51.9× 6.64e-4 1.15e-2 ✓ sig.
determination of bilateral symmetry
ALDH1A2
 GO:0009855 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure
RHOA
 GO:0001998 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
alpha-beta T cell lineage commitment
RHOA
 GO:0002363 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
mitotic cleavage furrow formation
RHOA
 GO:1903673 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
regulation of peptidyl-serine phosphorylation
NSD1
 GO:0033135 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
regulation of RNA polymerase II regulatory region sequence-specific DNA binding
NSD1
 GO:1903025 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
response to butyrate
PIK3CA
 GO:1903544 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.
hepatocyte homeostasis
EZH2
 GO:0036333 1 / 1 1,246× 8.03e-4 1.30e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Clapo syndrome Congenital malformation syndromes involving early overgrowth 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital intestinal duplication Congenital macrodactylia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital intestinal duplication Congenital malformation syndromes involving early overgrowth 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital intestinal duplication Hemifacial myohyperplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital macrodactylia Congenital malformation syndromes involving early overgrowth 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital macrodactylia Hemifacial myohyperplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cloves syndrome Hemifacial myohyperplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cloves syndrome Congenital malformation syndromes involving early overgrowth 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cloves syndrome Congenital macrodactylia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cloves syndrome Congenital intestinal duplication 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Clapo syndrome Hemifacial myohyperplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Clapo syndrome Congenital macrodactylia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Clapo syndrome Congenital intestinal duplication 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Clapo syndrome Cloves syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital malformation syndromes involving early overgrowth Hemifacial myohyperplasia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Clapo syndrome Hemihyperplasia multiple lipomatosis syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Cloves syndrome Hemihyperplasia multiple lipomatosis syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital intestinal duplication Hemihyperplasia multiple lipomatosis syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital macrodactylia Hemihyperplasia multiple lipomatosis syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Congenital malformation syndromes involving early overgrowth Hemihyperplasia multiple lipomatosis syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Capillary-lymphatic-venous malformation Cloves syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Capillary-lymphatic-venous malformation Clapo syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Capillary-lymphatic-venous malformation Congenital intestinal duplication 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Capillary-lymphatic-venous malformation Congenital macrodactylia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Capillary-lymphatic-venous malformation Congenital malformation syndromes involving early overgrowth 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital malformation syndromes involving early overgrowth Vascular malformation 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital macrodactylia Vascular malformation 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Congenital intestinal duplication Vascular malformation 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cloves syndrome Vascular malformation 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Clapo syndrome Vascular malformation 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Cloves syndrome Congenital hemihypertrophy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Charcot-Marie-Tooth disease type 2A1 Congenital hemihypertrophy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Charcot-Marie-Tooth disease type 4C Congenital hemihypertrophy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Clapo syndrome Congenital hemihypertrophy 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Congenital hemihypertrophy Congenital intestinal duplication 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Congenital malformation syndromes involving early overgrowth Diaphragmatic malformations 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital macrodactylia Diaphragmatic malformations 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital intestinal duplication Diaphragmatic malformations 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cloves syndrome Diaphragmatic malformations 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Upper extremity deformity, congenital Weaver syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Clapo syndrome Diaphragmatic malformations 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cohen-gibson syndrome Weaver syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Clapo syndrome Weaver syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Cloves syndrome Weaver syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.
Congenital intestinal duplication Weaver syndrome 0.167 1 3.25e-4 7.58e-4 ✓ sig.