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 442

6 diseases · 15 shared-gene connections
6 Diseases
10 Unique genes
0.322 Avg. similarity score
Decreased nerve conduction velocities 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 ⇵
Decreased nerve conduction velocities 5 5 1
Distal sensory loss 5 5 1
Hereditary ataxia 5 5 9
Hyporeflexia 5 5 1
Neurodegeneration, childhood-onset, with cerebellar atrophy 5 5 2
Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 5 5 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
ABHD12 6 / 6 Decreased nerve conduction velocities, Distal sensory loss, Hereditary ataxia, Hyporeflexia 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 ⇵
Vitamin E
TTPA
 Reactome 1 / 1 1,201× 8.33e-4 9.85e-3 ✓ sig.
Defective DHDDS causes retinitis pigmentosa 59
NUS1
 Reactome 1 / 2 601× 1.66e-3 1.66e-2 ✓ sig.
Response to elevated platelet cytosolic Ca2+
PRKCG
 Reactome 1 / 3 400× 2.50e-3 2.23e-2 ✓ sig.
Telomere C-strand (Lagging Strand) Synthesis
PCNA
 Reactome 1 / 5 240× 4.16e-3 3.21e-2 ✓ sig.
Arachidonate production from DAG
ABHD12
 Reactome 1 / 5 240× 4.16e-3 3.21e-2 ✓ sig.
Disinhibition of SNARE formation
PRKCG
 Reactome 1 / 5 240× 4.16e-3 3.21e-2 ✓ sig.
Synthesis of Dolichyl-phosphate
NUS1
 Reactome 1 / 6 200× 4.99e-3 3.64e-2 ✓ sig.
Calmodulin induced events
PRKCG
 Reactome 1 / 7 172× 5.82e-3 4.03e-2 ✓ sig.
Phase 1 - inactivation of fast Na+ channels
KCND3
 Reactome 1 / 7 172× 5.82e-3 4.03e-2 ✓ sig.
Spinocerebellar ataxia
KCND3, PRKCG
 KEGG 2 / 144 16.7× 6.03e-3 4.12e-2 ✓ sig.
Processive synthesis on the C-strand of the telomere
PCNA
 Reactome 1 / 8 150× 6.64e-3 4.39e-2 ✓ sig.
Hepatitis B
PCNA, PRKCG
 KEGG 2 / 163 14.7× 7.67e-3 4.82e-2 ✓ sig.
Processive synthesis on the lagging strand
PCNA
 Reactome 1 / 10 120× 8.30e-3 5.06e-2
Removal of the Flap Intermediate from the C-strand
PCNA
 Reactome 1 / 11 109× 9.12e-3 5.37e-2
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
PCNA
 Reactome 1 / 14 85.8× 1.16e-2 6.22e-2

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
adult walking behavior
AGTPBP1, ABHD12
 GO:0007628 2 / 34 110× 1.43e-4 4.00e-3 ✓ sig.
positive regulation of deoxyribonuclease activity
PCNA
 GO:0032077 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
negative regulation of establishment of blood-brain barrier
TTPA
 GO:0090212 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
developmental induction
NKX2-1
 GO:0031128 1 / 1 1,869× 5.35e-4 9.88e-3 ✓ sig.
lipid metabolic process
ABHD12, TTPA, NUS1, TPP1
 GO:0006629 4 / 840 8.9× 6.85e-4 1.17e-2 ✓ sig.
response to toxic substance
PRKCG, TTPA
 GO:0009636 2 / 83 45.0× 8.57e-4 1.33e-2 ✓ sig.
anterograde axonal transport of mitochondrion
AGTPBP1
 GO:0098957 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
forebrain neuron fate commitment
NKX2-1
 GO:0021877 1 / 2 934× 1.07e-3 1.51e-2 ✓ sig.
epithelial cell differentiation
PCNA, TPP1
 GO:0030855 2 / 110 34.0× 1.50e-3 1.82e-2 ✓ sig.
ventricular cardiac muscle cell membrane repolarization
KCND3
 GO:0099625 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
mitotic telomere maintenance via semi-conservative replication
PCNA
 GO:1902990 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
protein deglutamylation
AGTPBP1
 GO:0035608 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
retrograde axonal transport of mitochondrion
AGTPBP1
 GO:0098958 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
positive regulation of mismatch repair
PRKCG
 GO:0032425 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.
regulation of response to food
PRKCG
 GO:0032095 1 / 3 623× 1.60e-3 1.88e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Decreased nerve conduction velocities Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Decreased nerve conduction velocities Hyporeflexia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Decreased nerve conduction velocities Distal sensory loss 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Distal sensory loss Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Distal sensory loss Hyporeflexia 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Hyporeflexia Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Decreased nerve conduction velocities Neurodegeneration, childhood-onset, with cerebellar atrophy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Distal sensory loss Neurodegeneration, childhood-onset, with cerebellar atrophy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Hyporeflexia Neurodegeneration, childhood-onset, with cerebellar atrophy 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Neurodegeneration, childhood-onset, with cerebellar atrophy Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Decreased nerve conduction velocities Hereditary ataxia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Distal sensory loss Hereditary ataxia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Hereditary ataxia Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Hereditary ataxia Hyporeflexia 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Hereditary ataxia Neurodegeneration, childhood-onset, with cerebellar atrophy 0.091 1 1.16e-3 1.73e-3 ✓ sig.