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 229

7 diseases · 11 shared-gene connections
7 Diseases
44 Unique genes
0.258 Avg. similarity score
Congenital epicanthus Most-connected disease (5 links)
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Disease Searched: fibrodysplasia ossificans progressiva 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 epicanthus 5 5 14
ATP1A3-associated neurological disorder 4 4 1
Capos syndrome 4 4 1
Cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss 4 4 1
Alternating hemiplegia of childhood 3 3 2
Esophageal atresia 1 1 32
fibrodysplasia ossificans progressiva 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ATP1A3 6 / 7 Alternating hemiplegia of childhood, ATP1A3-associated neurological disorder, Capos syndrome, Cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss and 2 more
ACVR1 2 / 7 Congenital epicanthus, fibrodysplasia ossificans progressiva
KCNA6 2 / 7 Congenital epicanthus, Esophageal atresia
TCF4 2 / 7 Congenital epicanthus, Esophageal atresia
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 ⇵
Insulin secretion
ATP1A2, ATP1A3, CACNA1C, KCNN3
 KEGG 4 / 86 12.7× 2.67e-4 4.80e-3 ✓ sig.
Cardiac muscle contraction
ATP1A2, ATP1A3, MYH7, CACNA1C
 KEGG 4 / 87 12.5× 2.80e-4 4.96e-3 ✓ sig.
cGMP-PKG signaling pathway
ATP1A2, ATP1A3, MYH7, CACNA1C, INSR
 KEGG 5 / 166 8.2× 3.34e-4 5.72e-3 ✓ sig.
Aldosterone-regulated sodium reabsorption
ATP1A2, ATP1A3, INSR
 KEGG 3 / 38 21.5× 3.54e-4 6.01e-3 ✓ sig.
Leukocyte transendothelial migration
PTK2, PTPN11, ITGB1, SIPA1
 KEGG 4 / 116 9.4× 8.33e-4 1.16e-2 ✓ sig.
Ion homeostasis
ATP1A2, ATP1A3, ABCC9
 Reactome 3 / 54 15.2× 9.99e-4 1.34e-2 ✓ sig.
Thyroid hormone signaling pathway
ATP1A2, ATP1A3, MYH7, NOTCH1
 KEGG 4 / 122 8.9× 1.01e-3 1.35e-2 ✓ sig.
Adrenergic signaling in cardiomyocytes
ATP1A2, ATP1A3, MYH7, CACNA1C
 KEGG 4 / 154 7.1× 2.37e-3 2.58e-2 ✓ sig.
Proximal tubule bicarbonate reclamation
ATP1A2, ATP1A3
 KEGG 2 / 23 23.7× 3.16e-3 3.18e-2 ✓ sig.
Interleukin-3, Interleukin-5 and GM-CSF signaling
PTPN11, STAT5A
 Reactome 2 / 23 23.7× 3.16e-3 3.18e-2 ✓ sig.
Interleukin-20 family signaling
PTPN11, STAT5A
 Reactome 2 / 25 21.8× 3.73e-3 3.57e-2 ✓ sig.
Insulin receptor recycling
ATP6V0A1, INSR
 Reactome 2 / 26 21.0× 4.03e-3 3.78e-2 ✓ sig.
Downstream signal transduction
PTPN11, STAT5A
 Reactome 2 / 29 18.8× 5.00e-3 4.37e-2 ✓ sig.
MET activates PTK2 signaling
PTK2, ITGB1
 Reactome 2 / 30 18.2× 5.35e-3 4.58e-2 ✓ sig.
Aldosterone synthesis and secretion
ATP1A2, ATP1A3, CACNA1C
 KEGG 3 / 98 8.4× 5.48e-3 4.65e-2 ✓ 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 ⇵
potassium ion transport
ATP1A2, ATP1A3, ABCC9, KCNA6, KCNQ2, KCNN3
 GO:0006813 6 / 152 16.8× 1.43e-6 1.11e-4 ✓ sig.
cell communication by electrical coupling involved in cardiac conduction
ATP1A2, ATP1A3, CACNA1C
 GO:0086064 3 / 12 106× 2.64e-6 1.81e-4 ✓ sig.
negative regulation of anoikis
PTK2, ITGB1, NOTCH1
 GO:2000811 3 / 19 67.1× 1.15e-5 5.85e-4 ✓ sig.
potassium ion transmembrane transport
ATP1A2, ABCC9, KCNA6, KCNQ2, KCNN3
 GO:0071805 5 / 150 14.2× 2.63e-5 1.11e-3 ✓ sig.
heart development
ABCC9, ACVR1, PTPN11, CACNA1C, NOTCH1, TERT
 GO:0007507 6 / 273 9.3× 4.08e-5 1.55e-3 ✓ sig.
positive regulation of cardiac epithelial to mesenchymal transition
ACVR1, NOTCH1
 GO:0062043 2 / 5 170× 5.39e-5 1.91e-3 ✓ sig.
regulation of developmental process
KAT6B, ITGB1, NOTCH1
 GO:0050793 3 / 32 39.8× 5.76e-5 2.01e-3 ✓ sig.
positive regulation of autophagy
AMBRA1, MID2, PLK2, RPGR
 GO:0010508 4 / 92 18.5× 6.42e-5 2.18e-3 ✓ sig.
negative regulation of heart contraction
ATP1A2, PDE4D
 GO:0045822 2 / 6 142× 8.08e-5 2.59e-3 ✓ sig.
response to glycoside
ATP1A2, ATP1A3
 GO:1903416 2 / 6 142× 8.08e-5 2.59e-3 ✓ sig.
ATP metabolic process
ATP1A2, ABCC9, MYH7
 GO:0046034 3 / 36 35.4× 8.24e-5 2.63e-3 ✓ sig.
integrin-mediated signaling pathway
PTK2, PTPN11, DST, ITGB1
 GO:0007229 4 / 100 17.0× 8.89e-5 2.78e-3 ✓ sig.
positive regulation of D-glucose import
PTPN11, INSR, TERT
 GO:0046326 3 / 38 33.5× 9.70e-5 2.96e-3 ✓ sig.
positive regulation of bone mineralization
ACVR1, TFAP2A, TENT5A
 GO:0030501 3 / 42 30.3× 1.31e-4 3.72e-3 ✓ sig.
positive regulation of intracellular signal transduction
ACVR1, PTPN11, MID2
 GO:1902533 3 / 43 29.6× 1.41e-4 3.91e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Congenital epicanthus Esophageal atresia 0.068 3 2.92e-6 1.58e-5 ✓ sig.
ATP1A3-associated neurological disorder Capos syndrome 0.500 1 6.49e-5 2.33e-4 ✓ sig.
ATP1A3-associated neurological disorder Cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Capos syndrome Cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Alternating hemiplegia of childhood Capos syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Alternating hemiplegia of childhood Cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Alternating hemiplegia of childhood ATP1A3-associated neurological disorder 0.333 1 1.30e-4 3.93e-4 ✓ sig.
ATP1A3-associated neurological disorder Congenital epicanthus 0.067 1 9.09e-4 1.58e-3 ✓ sig.
Capos syndrome Congenital epicanthus 0.067 1 9.09e-4 1.58e-3 ✓ sig.
Cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss Congenital epicanthus 0.067 1 9.09e-4 1.58e-3 ✓ sig.
Congenital epicanthus fibrodysplasia ossificans progressiva 0.067 1 9.09e-4 1.58e-3 ✓ sig.