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 407

6 diseases · 14 shared-gene connections
6 Diseases
5 Unique genes
0.367 Avg. similarity score
Continuous spike and wave during sleep syndrome Most-connected disease (5 links)
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Disease Searched: Gastric mantle cell lymphoma 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 ⇵
Continuous spike and wave during sleep syndrome 5 5 1
Epilepsy with neurodevelopmental defects 5 5 1
Focal epilepsy with speech disorder and impaired intellectual development 5 5 1
Landau-kleffner syndrome 5 5 1
Continuous spike and wave during slow wave sleep syndrome 4 4 2
Gastric mantle cell lymphoma 4 4 4

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

Gene ⇵ Member diseases ⇵ Linked diseases
GRIN2A 6 / 6 Continuous spike and wave during sleep syndrome, Continuous spike and wave during slow wave sleep syndrome, Epilepsy with neurodevelopmental defects, Focal epilepsy with speech disorder and impaired intellectual development and 2 more
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 ⇵
MicroRNAs in cancer
CCND1, NOTCH1, ATM
 KEGG 3 / 311 23.2× 1.65e-4 2.83e-3 ✓ sig.
Human papillomavirus infection
CCND1, NOTCH1, ATM
 KEGG 3 / 333 21.6× 2.03e-4 3.32e-3 ✓ sig.
p53 signaling pathway
CCND1, ATM
 KEGG 2 / 75 64.1× 3.80e-4 5.40e-3 ✓ sig.
Endocrine resistance
CCND1, NOTCH1
 KEGG 2 / 99 48.5× 6.62e-4 8.28e-3 ✓ sig.
Thyroid hormone signaling pathway
CCND1, NOTCH1
 KEGG 2 / 122 39.4× 1.00e-3 1.14e-2 ✓ sig.
FoxO signaling pathway
CCND1, ATM
 KEGG 2 / 133 36.1× 1.19e-3 1.29e-2 ✓ sig.
Breast cancer
CCND1, NOTCH1
 KEGG 2 / 148 32.5× 1.47e-3 1.52e-2 ✓ sig.
Cellular senescence
CCND1, ATM
 KEGG 2 / 157 30.6× 1.65e-3 1.66e-2 ✓ sig.
Cell cycle
CCND1, ATM
 KEGG 2 / 158 30.4× 1.68e-3 1.67e-2 ✓ sig.
Defective LFNG causes SCDO3
NOTCH1
 Reactome 1 / 5 480× 2.08e-3 1.96e-2 ✓ sig.
Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling
NOTCH1
 Reactome 1 / 5 480× 2.08e-3 1.96e-2 ✓ sig.
Sensing of DNA Double Strand Breaks
ATM
 Reactome 1 / 6 400× 2.50e-3 2.23e-2 ✓ sig.
PTK6 Regulates Cell Cycle
CCND1
 Reactome 1 / 6 400× 2.50e-3 2.23e-2 ✓ sig.
Pre-NOTCH Processing in Golgi
NOTCH1
 Reactome 1 / 6 400× 2.50e-3 2.23e-2 ✓ sig.
Assembly and cell surface presentation of NMDA receptors
GRIN2A
 Reactome 1 / 6 400× 2.50e-3 2.23e-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 ⇵
animal organ regeneration
CCND1, NOTCH1
 GO:0031100 2 / 28 267× 2.16e-5 9.80e-4 ✓ sig.
positive regulation of apoptotic process
GRIN2A, NOTCH1, ATM
 GO:0043065 3 / 326 34.4× 5.13e-5 1.88e-3 ✓ sig.
liver development
CCND1, NOTCH1
 GO:0001889 2 / 87 85.9× 2.12e-4 5.31e-3 ✓ sig.
protein catabolic process
GRIN2A, NOTCH1
 GO:0030163 2 / 97 77.1× 2.64e-4 6.20e-3 ✓ sig.
coronary sinus valve morphogenesis
NOTCH1
 GO:0003182 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
regulation of cardioblast proliferation
NOTCH1
 GO:0003264 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation
NOTCH1
 GO:0003270 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
foregut morphogenesis
NOTCH1
 GO:0007440 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
venous endothelial cell differentiation
NOTCH1
 GO:0060843 1 / 1 3,737× 2.68e-4 6.25e-3 ✓ sig.
response to ethanol
GRIN2A, CCND1
 GO:0045471 2 / 110 68.0× 3.39e-4 7.32e-3 ✓ sig.
endocardium morphogenesis
NOTCH1
 GO:0003160 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
coronary vein morphogenesis
NOTCH1
 GO:0003169 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
cardiac right atrium morphogenesis
NOTCH1
 GO:0003213 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
growth involved in heart morphogenesis
NOTCH1
 GO:0003241 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.
negative regulation of cell proliferation involved in heart valve morphogenesis
NOTCH1
 GO:0003252 1 / 2 1,869× 5.35e-4 9.88e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Continuous spike and wave during sleep syndrome Focal epilepsy with speech disorder and impaired intellectual development 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Continuous spike and wave during sleep syndrome Landau-kleffner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Continuous spike and wave during sleep syndrome Epilepsy with neurodevelopmental defects 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epilepsy with neurodevelopmental defects Focal epilepsy with speech disorder and impaired intellectual development 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Epilepsy with neurodevelopmental defects Landau-kleffner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Focal epilepsy with speech disorder and impaired intellectual development Landau-kleffner syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Continuous spike and wave during sleep syndrome Continuous spike and wave during slow wave sleep syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Continuous spike and wave during slow wave sleep syndrome Focal epilepsy with speech disorder and impaired intellectual development 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Continuous spike and wave during slow wave sleep syndrome Landau-kleffner syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Continuous spike and wave during slow wave sleep syndrome Epilepsy with neurodevelopmental defects 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Continuous spike and wave during sleep syndrome Gastric mantle cell lymphoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Epilepsy with neurodevelopmental defects Gastric mantle cell lymphoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Focal epilepsy with speech disorder and impaired intellectual development Gastric mantle cell lymphoma 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Gastric mantle cell lymphoma Landau-kleffner syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.