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.

← Back to all clusters

Cluster 173

9 diseases · 11 shared-gene connections
9 Diseases
25 Unique genes
0.080 Avg. similarity score
Hereditary sensory and autonomic neuropathy Most-connected disease (8 links)
Log in to save this analysis

Save This Analysis

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 ⇵
Hereditary sensory and autonomic neuropathy 8 8 19
Sensory neuropathy 4 4 13
Peho syndrome 2 2 2
hereditary sensory and autonomic neuropathy type 4 2 2 1
neuropathy, hereditary sensory and autonomic, type 2A 2 2 1
Hereditary sensory and autonomic neuropathy with spastic paraplegia 1 1 1
neuropathy, hereditary sensory and autonomic, type 1A 1 1 1
neuropathy, hereditary sensory and autonomic, type 1C 1 1 1
neuropathy, hereditary sensory, type 1F 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
KIF1A 3 / 9 Hereditary sensory and autonomic neuropathy, Peho syndrome, Sensory neuropathy
NTRK1 3 / 9 Hereditary sensory and autonomic neuropathy, hereditary sensory and autonomic neuropathy type 4, Sensory neuropathy
WNK1 3 / 9 Hereditary sensory and autonomic neuropathy, neuropathy, hereditary sensory and autonomic, type 2A, Sensory neuropathy
ATL3 2 / 9 Hereditary sensory and autonomic neuropathy, neuropathy, hereditary sensory, type 1F
CCT5 2 / 9 Hereditary sensory and autonomic neuropathy, Hereditary sensory and autonomic neuropathy with spastic paraplegia
DNMT1 2 / 9 Hereditary sensory and autonomic neuropathy, Sensory neuropathy
FLVCR1 2 / 9 Hereditary sensory and autonomic neuropathy, Sensory neuropathy
NGF 2 / 9 Hereditary sensory and autonomic neuropathy, Sensory neuropathy
RETREG1 2 / 9 Hereditary sensory and autonomic neuropathy, Sensory neuropathy
SCN11A 2 / 9 Hereditary sensory and autonomic neuropathy, Sensory neuropathy
SPTLC1 2 / 9 Hereditary sensory and autonomic neuropathy, neuropathy, hereditary sensory and autonomic, type 1A
SPTLC2 2 / 9 Hereditary sensory and autonomic neuropathy, neuropathy, hereditary sensory and autonomic, type 1C
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 ⇵
TRKA activation by NGF
NGF, NTRK1
 Reactome 2 / 2 480× 4.16e-6 1.63e-4 ✓ sig.
ARMS-mediated activation
NGF, NTRK1
 Reactome 2 / 5 192× 4.14e-5 1.10e-3 ✓ sig.
Sphingolipid de novo biosynthesis
SPTLC1, SPTLC2, SPTLC3
 Reactome 3 / 43 33.5× 9.31e-5 2.12e-3 ✓ sig.
PI3K/AKT activation
NGF, NTRK1
 Reactome 2 / 9 107× 1.48e-4 3.09e-3 ✓ sig.
Sphingolipid metabolism
SPTLC1, SPTLC2, SPTLC3
 KEGG 3 / 54 26.7× 1.84e-4 3.68e-3 ✓ sig.
Retrograde neurotrophin signalling
NGF, NTRK1
 Reactome 2 / 11 87.3× 2.26e-4 4.32e-3 ✓ sig.
Frs2-mediated activation
NGF, NTRK1
 Reactome 2 / 12 80.1× 2.71e-4 4.96e-3 ✓ sig.
Sphingolipid signaling pathway
SPTLC1, SPTLC2, SPTLC3
 KEGG 3 / 122 11.8× 2.00e-3 2.28e-2 ✓ sig.
Oligomerization of connexins into connexons
GJB1
 Reactome 1 / 1 480× 2.08e-3 2.35e-2 ✓ sig.
Phase 0 - rapid depolarisation
SCN11A, SCN9A
 Reactome 2 / 44 21.8× 3.73e-3 3.59e-2 ✓ sig.
NFG and proNGF binds to p75NTR
NGF
 Reactome 1 / 2 240× 4.16e-3 3.87e-2 ✓ sig.
Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2
POMT1
 Reactome 1 / 3 160× 6.23e-3 5.06e-2
Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1
POMT1
 Reactome 1 / 3 160× 6.23e-3 5.06e-2
SUMOylation of DNA methylation proteins
DNMT1
 Reactome 1 / 4 120× 8.30e-3 6.10e-2
Axonal growth stimulation
NGF
 Reactome 1 / 4 120× 8.30e-3 6.10e-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 ⇵
sensory perception of pain
SCN11A, NGF, PRDM12, RETREG1, SCN9A
 GO:0019233 5 / 44 84.9× 2.94e-9 5.79e-7 ✓ sig.
detection of temperature stimulus involved in sensory perception of pain
SCN11A, NTRK1, PRDM12, SCN9A
 GO:0050965 4 / 20 149× 1.19e-8 1.99e-6 ✓ sig.
sphingosine biosynthetic process
SPTLC1, SPTLC2, SPTLC3
 GO:0046512 3 / 16 140× 1.17e-6 9.41e-5 ✓ sig.
sphinganine biosynthetic process
SPTLC1, SPTLC2
 GO:0046511 2 / 2 747× 1.72e-6 1.28e-4 ✓ sig.
circadian rhythm
SCN11A, NGF, NTRK1, SCN9A
 GO:0007623 4 / 82 36.5× 4.06e-6 2.54e-4 ✓ sig.
behavioral response to formalin induced pain
SCN11A, NTRK1
 GO:0061368 2 / 3 498× 5.15e-6 3.08e-4 ✓ sig.
positive regulation of lipophagy
SPTLC1, SPTLC2
 GO:1904504 2 / 5 299× 1.71e-5 7.95e-4 ✓ sig.
endoplasmic reticulum membrane fusion
ATL1, ATL3
 GO:0016320 2 / 5 299× 1.71e-5 7.95e-4 ✓ sig.
ceramide biosynthetic process
SPTLC1, SPTLC2, SPTLC3
 GO:0046513 3 / 41 54.7× 2.18e-5 9.61e-4 ✓ sig.
sphingolipid biosynthetic process
SPTLC1, SPTLC2, SPTLC3
 GO:0030148 3 / 45 49.8× 2.89e-5 1.19e-3 ✓ sig.
endoplasmic reticulum organization
RETREG1, ATL1, ATL3
 GO:0007029 3 / 46 48.7× 3.09e-5 1.25e-3 ✓ sig.
detection of mechanical stimulus involved in sensory perception
SCN11A, SCN9A
 GO:0050974 2 / 8 187× 4.79e-5 1.74e-3 ✓ sig.
endoplasmic reticulum tubular network membrane organization
ATL1, ATL3
 GO:1990809 2 / 8 187× 4.79e-5 1.74e-3 ✓ sig.
sphingolipid metabolic process
SPTLC1, SPTLC2, SPTLC3
 GO:0006665 3 / 59 38.0× 6.54e-5 2.20e-3 ✓ sig.
sphingomyelin biosynthetic process
SPTLC1, SPTLC2
 GO:0006686 2 / 11 136× 9.38e-5 2.88e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hereditary sensory and autonomic neuropathy Sensory neuropathy 0.320 8 1.24e-21 2.70e-20 ✓ sig.
hereditary sensory and autonomic neuropathy type 4 Sensory neuropathy 0.071 1 8.44e-4 1.48e-3 ✓ sig.
neuropathy, hereditary sensory and autonomic, type 2A Sensory neuropathy 0.071 1 8.44e-4 1.48e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy hereditary sensory and autonomic neuropathy type 4 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy Hereditary sensory and autonomic neuropathy with spastic paraplegia 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy neuropathy, hereditary sensory and autonomic, type 1A 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy neuropathy, hereditary sensory and autonomic, type 1C 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy neuropathy, hereditary sensory and autonomic, type 2A 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy neuropathy, hereditary sensory, type 1F 0.050 1 1.23e-3 1.97e-3 ✓ sig.
Peho syndrome Sensory neuropathy 0.067 1 1.69e-3 2.51e-3 ✓ sig.
Hereditary sensory and autonomic neuropathy Peho syndrome 0.048 1 2.47e-3 3.36e-3 ✓ sig.