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 150

10 diseases · 17 shared-gene connections
10 Diseases
11 Unique genes
0.281 Avg. similarity score
Dysgenesis of corpus callosum Most-connected disease (6 links)
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Disease Searched: Delayed psychomotor development 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 ⇵
Dysgenesis of corpus callosum 6 6 4
17q21.31 microdeletion syndrome 5 5 1
Chromosome 17 deletion 5 5 2
Koolen-de vries syndrome 5 5 1
Chromosome 17q21.31 deletion syndrome 3 3 3
Delayed psychomotor development 3 3 2
Juvenile myoclonic epilepsy 3 3 4
Endocrine-cerebroosteodysplasia 2 2 1
Juvenile absence epilepsy 1 1 1
Multiple congenital anomalies-neurodevelopmental syndrome, x-linked 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KANSL1 6 / 10 17q21.31 microdeletion syndrome, Chromosome 17 deletion, Chromosome 17q21.31 deletion syndrome, Delayed psychomotor development and 2 more
CILK1 3 / 10 Dysgenesis of corpus callosum, Endocrine-cerebroosteodysplasia, Juvenile myoclonic epilepsy
EFHC1 2 / 10 Juvenile absence epilepsy, Juvenile myoclonic epilepsy
OTUD5 2 / 10 Dysgenesis of corpus callosum, Multiple congenital anomalies-neurodevelopmental syndrome, x-linked
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 ⇵
Stabilization of p53
TP53, ATM
 Reactome 2 / 11 199× 4.18e-5 9.47e-4 ✓ sig.
TP53 Regulates Transcription of Caspase Activators and Caspases
TP53, ATM
 Reactome 2 / 12 182× 5.01e-5 1.09e-3 ✓ sig.
Regulation of TP53 Activity through Methylation
TP53, ATM
 Reactome 2 / 19 115× 1.29e-4 2.32e-3 ✓ sig.
TP53 Regulates Transcription of Genes Involved in Cytochrome C Release
TP53, ATM
 Reactome 2 / 20 109× 1.44e-4 2.53e-3 ✓ sig.
Regulation of TP53 Degradation
TP53, ATM
 Reactome 2 / 36 60.7× 4.72e-4 6.40e-3 ✓ sig.
Ovarian tumor domain proteases
TP53, OTUD5
 Reactome 2 / 38 57.5× 5.27e-4 6.95e-3 ✓ sig.
Autodegradation of the E3 ubiquitin ligase COP1
TP53, ATM
 Reactome 2 / 52 42.0× 9.86e-4 1.12e-2 ✓ sig.
TP53 Regulates Transcription of DNA Repair Genes
TP53, ATM
 Reactome 2 / 65 33.6× 1.54e-3 1.57e-2 ✓ sig.
DNA Damage/Telomere Stress Induced Senescence
TP53, ATM
 Reactome 2 / 66 33.1× 1.58e-3 1.60e-2 ✓ sig.
Regulation of TP53 Expression
TP53
 Reactome 1 / 2 546× 1.83e-3 1.78e-2 ✓ sig.
Platinum drug resistance
TP53, ATM
 KEGG 2 / 75 29.1× 2.04e-3 1.93e-2 ✓ sig.
p53 signaling pathway
TP53, ATM
 KEGG 2 / 75 29.1× 2.04e-3 1.93e-2 ✓ sig.
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
TP53, ATM
 Reactome 2 / 76 28.7× 2.09e-3 1.97e-2 ✓ sig.
MAPK signaling pathway
TP53, FLNA, CACNB4
 KEGG 3 / 299 11.0× 2.17e-3 2.02e-2 ✓ sig.
G2/M DNA damage checkpoint
TP53, ATM
 Reactome 2 / 84 26.0× 2.55e-3 2.27e-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 ⇵
replicative senescence
TP53, ATM
 GO:0090399 2 / 16 212× 3.76e-5 1.49e-3 ✓ sig.
cellular response to gamma radiation
TP53, ATM
 GO:0071480 2 / 28 121× 1.18e-4 3.49e-3 ✓ sig.
gamma-aminobutyric acid signaling pathway
GABRA1, CACNB4
 GO:0007214 2 / 30 113× 1.36e-4 3.84e-3 ✓ sig.
determination of adult lifespan
TP53, ATM
 GO:0008340 2 / 38 89.4× 2.19e-4 5.40e-3 ✓ sig.
cellular response to stress
TP53, ATM
 GO:0033554 2 / 45 75.5× 3.08e-4 6.90e-3 ✓ sig.
response to ionizing radiation
TP53, ATM
 GO:0010212 2 / 47 72.3× 3.36e-4 7.26e-3 ✓ sig.
DNA damage response, signal transduction by p53 class mediator
TP53, ATM
 GO:0030330 2 / 48 70.8× 3.50e-4 7.49e-3 ✓ sig.
protein stabilization
TP53, ATM, FLNA
 GO:0050821 3 / 248 20.6× 3.52e-4 7.52e-3 ✓ sig.
thymus development
ATM, CACNB4
 GO:0048538 2 / 50 68.0× 3.80e-4 7.89e-3 ✓ sig.
somitogenesis
TP53, ATM
 GO:0001756 2 / 50 68.0× 3.80e-4 7.89e-3 ✓ sig.
cellular senescence
TP53, ATM
 GO:0090398 2 / 57 59.6× 4.94e-4 9.41e-3 ✓ sig.
negative regulation of helicase activity
TP53
 GO:0051097 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator
TP53
 GO:1902253 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
negative regulation of G1 to G0 transition
TP53
 GO:1903451 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.
regulation of membrane repolarization during atrial cardiac muscle cell action potential
FLNA
 GO:1905000 1 / 1 1,699× 5.89e-4 1.06e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
17q21.31 microdeletion syndrome Koolen-de vries syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
17q21.31 microdeletion syndrome Chromosome 17 deletion 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chromosome 17 deletion Koolen-de vries syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
17q21.31 microdeletion syndrome Delayed psychomotor development 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Chromosome 17 deletion Delayed psychomotor development 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Delayed psychomotor development Koolen-de vries syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
17q21.31 microdeletion syndrome Chromosome 17q21.31 deletion syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Chromosome 17 deletion Chromosome 17q21.31 deletion syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Chromosome 17q21.31 deletion syndrome Koolen-de vries syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Dysgenesis of corpus callosum Multiple congenital anomalies-neurodevelopmental syndrome, x-linked 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Juvenile absence epilepsy Juvenile myoclonic epilepsy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Endocrine-cerebroosteodysplasia Juvenile myoclonic epilepsy 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysgenesis of corpus callosum Endocrine-cerebroosteodysplasia 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysgenesis of corpus callosum Koolen-de vries syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Chromosome 17 deletion Dysgenesis of corpus callosum 0.200 1 2.58e-4 5.38e-4 ✓ sig.
17q21.31 microdeletion syndrome Dysgenesis of corpus callosum 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Dysgenesis of corpus callosum Juvenile myoclonic epilepsy 0.125 1 1.03e-3 1.57e-3 ✓ sig.