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 488

6 diseases · 15 shared-gene connections
6 Diseases
1 Unique genes
0.500 Avg. similarity score
Chronic pain Most-connected disease (5 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 ⇵
Chronic pain 5 5 1
Erythermalgia, primary 5 5 1
Hereditary sensory and autonomic neuropathy type 2d 5 5 1
Indifference to pain, congenital, autosomal recessive 5 5 1
Primary erythromelalgia 5 5 1
Small fiber neuropathy, ad 5 5 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SCN9A 6 / 6 Chronic pain, Erythermalgia, primary, Hereditary sensory and autonomic neuropathy type 2d, Indifference to pain, congenital, autosomal recessive 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 ⇵
Phase 0 - rapid depolarisation
SCN9A
 Reactome 1 / 44 273× 3.66e-3 2.93e-2 ✓ sig.
Taste transduction
SCN9A
 KEGG 1 / 86 140× 7.16e-3 4.61e-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 ⇵
action potential propagation
SCN9A
 GO:0098870 1 / 1 18,687× 5.35e-5 1.94e-3 ✓ sig.
detection of mechanical stimulus involved in sensory perception
SCN9A
 GO:0050974 1 / 8 2,336× 4.28e-4 8.53e-3 ✓ sig.
behavioral response to pain
SCN9A
 GO:0048266 1 / 18 1,038× 9.63e-4 1.42e-2 ✓ sig.
detection of temperature stimulus involved in sensory perception of pain
SCN9A
 GO:0050965 1 / 20 934× 1.07e-3 1.51e-2 ✓ sig.
cardiac muscle cell action potential involved in contraction
SCN9A
 GO:0086002 1 / 24 779× 1.28e-3 1.67e-2 ✓ sig.
neuronal action potential
SCN9A
 GO:0019228 1 / 34 550× 1.82e-3 2.02e-2 ✓ sig.
sensory perception of pain
SCN9A
 GO:0019233 1 / 44 425× 2.35e-3 2.30e-2 ✓ sig.
action potential
SCN9A
 GO:0001508 1 / 53 353× 2.84e-3 2.54e-2 ✓ sig.
post-embryonic development
SCN9A
 GO:0009791 1 / 82 228× 4.39e-3 3.15e-2 ✓ sig.
circadian rhythm
SCN9A
 GO:0007623 1 / 82 228× 4.39e-3 3.15e-2 ✓ sig.
response to toxic substance
SCN9A
 GO:0009636 1 / 83 225× 4.44e-3 3.17e-2 ✓ sig.
sodium ion transmembrane transport
SCN9A
 GO:0035725 1 / 134 139× 7.17e-3 3.98e-2 ✓ sig.
sodium ion transport
SCN9A
 GO:0006814 1 / 144 130× 7.71e-3 4.10e-2 ✓ sig.
monoatomic ion transmembrane transport
SCN9A
 GO:0034220 1 / 404 46.3× 2.16e-2 6.78e-2
inflammatory response
SCN9A
 GO:0006954 1 / 467 40.0× 2.50e-2 7.35e-2

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Chronic pain Primary erythromelalgia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chronic pain Erythermalgia, primary 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chronic pain Small fiber neuropathy, ad 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chronic pain Hereditary sensory and autonomic neuropathy type 2d 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Chronic pain Indifference to pain, congenital, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythermalgia, primary Primary erythromelalgia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythermalgia, primary Small fiber neuropathy, ad 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythermalgia, primary Hereditary sensory and autonomic neuropathy type 2d 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Erythermalgia, primary Indifference to pain, congenital, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hereditary sensory and autonomic neuropathy type 2d Primary erythromelalgia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hereditary sensory and autonomic neuropathy type 2d Small fiber neuropathy, ad 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hereditary sensory and autonomic neuropathy type 2d Indifference to pain, congenital, autosomal recessive 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Indifference to pain, congenital, autosomal recessive Primary erythromelalgia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Indifference to pain, congenital, autosomal recessive Small fiber neuropathy, ad 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Primary erythromelalgia Small fiber neuropathy, ad 0.500 1 6.46e-5 1.98e-4 ✓ sig.