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 328

6 diseases · 8 shared-gene connections
6 Diseases
33 Unique genes
0.188 Avg. similarity score
Infantile spasms Most-connected disease (4 links)
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Disease Searched: Infantile spasms 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 ⇵
Infantile spasms 4 4 11
West syndrome 4 4 30
Beta-ureidopropionase deficiency 3 3 1
Cryptogenic west syndrome 3 3 8
Epilepsy due to perinatal stroke 1 1 1
medium chain acyl-coa dehydrogenase deficiency 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
UPB1 4 / 6 Beta-ureidopropionase deficiency, Cryptogenic west syndrome, Infantile spasms, West syndrome
CRH 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
HSD17B4 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
MC2R 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
POMC 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
STXBP1 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
TSC1 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
TSC2 3 / 6 Cryptogenic west syndrome, Infantile spasms, West syndrome
ACADM 2 / 6 Infantile spasms, medium chain acyl-coa dehydrogenase deficiency
ST3GAL3 2 / 6 Epilepsy due to perinatal stroke, West syndrome
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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Nef mediated downregulation of MHC class I complex cell surface expression
AP1S2
 Reactome 1 / 10 85.8× 1.16e-2 7.60e-2
CD28 dependent Vav1 pathway
PAK3
 Reactome 1 / 12 71.5× 1.39e-2 8.47e-2
Sema3A PAK dependent Axon repulsion
PAK3
 Reactome 1 / 15 57.2× 1.74e-2 9.69e-2
Major pathway of rRNA processing in the nucleolus and cytosol
LAS1L, RPL10
 Reactome 2 / 184 9.3× 1.88e-2 1.02e-1
Ephrin signaling
PAK3
 Reactome 1 / 19 45.2× 2.19e-2 1.11e-1
CD209 (DC-SIGN) signaling
PAK3
 Reactome 1 / 21 40.9× 2.42e-2 1.17e-1
Human immunodeficiency virus 1 infection
AP1S2, PAK3
 KEGG 2 / 213 8.1× 2.48e-2 1.18e-1
Downregulation of SMAD2/3:SMAD4 transcriptional activity
USP9X
 Reactome 1 / 22 39.0× 2.54e-2 1.20e-1
RHO GTPases activate PAKs
PAK3
 Reactome 1 / 23 37.3× 2.65e-2 1.23e-1
Dopamine Neurotransmitter Release Cycle
CASK
 Reactome 1 / 23 37.3× 2.65e-2 1.23e-1
VEGFR2 mediated vascular permeability
PAK3
 Reactome 1 / 29 29.6× 3.33e-2 1.40e-1
Synthesis of active ubiquitin: roles of E1 and E2 enzymes
USP9X
 Reactome 1 / 30 28.6× 3.44e-2 1.42e-1
Generation of second messenger molecules
PAK3
 Reactome 1 / 31 27.7× 3.56e-2 1.45e-1
Neurexins and neuroligins
CASK
 Reactome 1 / 32 26.8× 3.67e-2 1.48e-1
Lysosome Vesicle Biogenesis
AP1S2
 Reactome 1 / 35 24.5× 4.01e-2 1.55e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
cerebral cortex development
TSC1, NTRK2, PHACTR1, PLCB1, TUBA1A
 GO:0021987 5 / 88 32.2× 4.42e-7 4.33e-5 ✓ sig.
action potential
KCNQ2, SCN1A, SCN2A, SCN8A
 GO:0001508 4 / 53 42.7× 2.22e-6 1.62e-4 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN1A, SCN2A, SCN8A
 GO:0086002 3 / 24 70.8× 9.90e-6 5.36e-4 ✓ sig.
cardiac muscle cell differentiation
TSC1, ACADM, SIK1
 GO:0055007 3 / 30 56.6× 1.97e-5 9.18e-4 ✓ sig.
neuron apoptotic process
CRH, STXBP1, SCN2A, TUBA1A
 GO:0051402 4 / 98 23.1× 2.59e-5 1.13e-3 ✓ sig.
neuron migration
ARX, CDKL5, NTRK2, TUBA1A
 GO:0001764 4 / 132 17.2× 8.30e-5 2.74e-3 ✓ sig.
neuronal action potential propagation
NTRK2, SCN1A
 GO:0019227 2 / 11 103× 1.65e-4 4.52e-3 ✓ sig.
anoikis
TSC2, SIK1
 GO:0043276 2 / 12 94.4× 1.97e-4 5.17e-3 ✓ sig.
long-term synaptic potentiation
CRH, GRIN2B, NTRK2
 GO:0060291 3 / 71 23.9× 2.64e-4 6.35e-3 ✓ sig.
myelination
TSC1, SCN2A, SCN8A
 GO:0042552 3 / 73 23.3× 2.87e-4 6.73e-3 ✓ sig.
locomotory exploration behavior
CRH, TUBA1A
 GO:0035641 2 / 16 70.8× 3.57e-4 7.83e-3 ✓ sig.
memory
PLCB1, SCN2A, TUBA1A
 GO:0007613 3 / 87 19.5× 4.81e-4 9.61e-3 ✓ sig.
glutamate receptor signaling pathway
GRIN2B, PLCB1
 GO:0007215 2 / 19 59.6× 5.08e-4 9.99e-3 ✓ sig.
cellular response to starvation
TSC1, TSC2, WDR45
 GO:0009267 3 / 90 18.9× 5.31e-4 1.03e-2 ✓ sig.
monoatomic ion transmembrane transport
GRIN2B, KCNQ2, SCN1A, SCN2A, SCN8A
 GO:0034220 5 / 404 7.0× 6.64e-4 1.19e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Cryptogenic west syndrome Infantile spasms 0.667 8 2.11e-27 5.80e-26 ✓ sig.
Cryptogenic west syndrome West syndrome 0.258 8 7.48e-23 1.61e-21 ✓ sig.
Infantile spasms West syndrome 0.235 8 1.23e-20 2.42e-19 ✓ sig.
Beta-ureidopropionase deficiency Cryptogenic west syndrome 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Beta-ureidopropionase deficiency Infantile spasms 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Infantile spasms medium chain acyl-coa dehydrogenase deficiency 0.083 1 7.14e-4 1.34e-3 ✓ sig.
Beta-ureidopropionase deficiency West syndrome 0.032 1 1.95e-3 2.83e-3 ✓ sig.
Epilepsy due to perinatal stroke West syndrome 0.032 1 1.95e-3 2.83e-3 ✓ sig.