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 602

5 diseases · 7 shared-gene connections
5 Diseases
2 Unique genes
0.405 Avg. similarity score
Dyskinesia, limb and orofacial, infantile-onset Most-connected disease (4 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 ⇵
Dyskinesia, limb and orofacial, infantile-onset 4 4 2
Childhood-onset chorea with bilateral striatal lesions 3 3 1
Striatal degeneration, autosomal dominant 3 3 1
Striatal degeneration, autosomal dominant 2 3 3 1
Childhood-onset benign chorea with striatal involvement 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
LINC00473 4 / 5 Childhood-onset chorea with bilateral striatal lesions, Dyskinesia, limb and orofacial, infantile-onset, Striatal degeneration, autosomal dominant, Striatal degeneration, autosomal dominant 2
PDE10A 2 / 5 Childhood-onset benign chorea with striatal involvement, Dyskinesia, limb and orofacial, infantile-onset
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 ⇵
cGMP effects
PDE10A
 Reactome 1 / 11 546× 1.83e-3 1.78e-2 ✓ sig.
Morphine addiction
PDE10A
 KEGG 1 / 91 66.0× 1.51e-2 7.28e-2
Purine metabolism
PDE10A
 KEGG 1 / 128 46.9× 2.12e-2 8.86e-2
G alpha (s) signalling events
PDE10A
 Reactome 1 / 140 42.9× 2.32e-2 9.33e-2
cAMP signaling pathway
PDE10A
 KEGG 1 / 226 26.6× 3.73e-2 1.22e-1
Metabolic pathways
PDE10A
 KEGG 1 / 1,563 3.8× 2.43e-1 3.76e-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 ⇵
regulation of cAMP/PKA signal transduction
PDE10A
 GO:0141161 1 / 5 1,869× 5.35e-4 9.88e-3 ✓ sig.
cGMP catabolic process
PDE10A
 GO:0046069 1 / 5 1,869× 5.35e-4 9.88e-3 ✓ sig.
regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway
PDE10A
 GO:0106070 1 / 5 1,869× 5.35e-4 9.88e-3 ✓ sig.
negative regulation of cGMP-mediated signaling
PDE10A
 GO:0010754 1 / 6 1,557× 6.42e-4 1.11e-2 ✓ sig.
cAMP catabolic process
PDE10A
 GO:0006198 1 / 9 1,038× 9.63e-4 1.42e-2 ✓ sig.
negative regulation of cAMP/PKA signal transduction
PDE10A
 GO:0141162 1 / 28 334× 2.99e-3 2.59e-2 ✓ sig.
DNA-templated transcription
LINC00473
 GO:0006351 1 / 113 82.7× 1.21e-2 5.08e-2
signal transduction
PDE10A
 GO:0007165 1 / 2,125 4.4× 2.15e-1 2.80e-1

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Childhood-onset chorea with bilateral striatal lesions Striatal degeneration, autosomal dominant 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Childhood-onset chorea with bilateral striatal lesions Striatal degeneration, autosomal dominant 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Striatal degeneration, autosomal dominant Striatal degeneration, autosomal dominant 2 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Childhood-onset benign chorea with striatal involvement Dyskinesia, limb and orofacial, infantile-onset 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Childhood-onset chorea with bilateral striatal lesions Dyskinesia, limb and orofacial, infantile-onset 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Dyskinesia, limb and orofacial, infantile-onset Striatal degeneration, autosomal dominant 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Dyskinesia, limb and orofacial, infantile-onset Striatal degeneration, autosomal dominant 2 0.333 1 1.29e-4 3.27e-4 ✓ sig.