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 118

11 diseases · 17 shared-gene connections
11 Diseases
24 Unique genes
0.178 Avg. similarity score
Autosomal dominant nonsyndromic hearing loss Most-connected disease (6 links)
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Disease Searched: Spondyloepiphyseal dysplasia with congenital joint dislocations 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 ⇵
Autosomal dominant nonsyndromic hearing loss 6 6 12
Deafness, autosomal dominant 37 5 5 1
Fibrochondrogenesis 5 5 1
Fibrochondrogenesis 1 5 5 1
Intervertebral disc displacement 4 4 5
Peritoneal disease 4 4 9
Deafness, autosomal dominant 21 1 1 1
Deafness, autosomal dominant 7 1 1 1
Deafness, autosomal dominant, 77 1 1 1
Mitochondrial dna depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria) 1 1 1
Spondyloepiphyseal dysplasia with congenital joint dislocations 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
COL11A1 6 / 11 Autosomal dominant nonsyndromic hearing loss, Deafness, autosomal dominant 37, Fibrochondrogenesis, Fibrochondrogenesis 1 and 2 more
ABCC1 2 / 11 Autosomal dominant nonsyndromic hearing loss, Deafness, autosomal dominant, 77
CHST3 2 / 11 Intervertebral disc displacement, Spondyloepiphyseal dysplasia with congenital joint dislocations
LMX1A 2 / 11 Autosomal dominant nonsyndromic hearing loss, Deafness, autosomal dominant 7
RIPOR2 2 / 11 Autosomal dominant nonsyndromic hearing loss, Deafness, autosomal dominant 21
SUCLA2 2 / 11 Mitochondrial dna depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria), Peritoneal disease
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 ⇵
Ion transport by P-type ATPases
ATP2B2, ATP11A
 Reactome 2 / 56 17.9× 5.52e-3 3.69e-2 ✓ sig.
Cytoskeleton in muscle cells
COL11A1, THBS2, ACTG1
 KEGG 3 / 232 6.5× 1.07e-2 5.67e-2
ABC-family proteins mediated transport
ABCC1, PSMC3
 Reactome 2 / 81 12.4× 1.13e-2 5.87e-2
Cam-PDE 1 activation
PDE1C
 Reactome 1 / 6 83.4× 1.19e-2 6.06e-2
Calcium signaling pathway
ERBB4, ATP2B2, PDE1C
 KEGG 3 / 254 5.9× 1.36e-2 6.60e-2
Salivary secretion
AMY1C, ATP2B2
 KEGG 2 / 93 10.8× 1.47e-2 6.89e-2
Defective CHST3 causes SEDCJD
CHST3
 Reactome 1 / 8 62.6× 1.59e-2 7.23e-2
Pancreatic secretion
AMY1C, ATP2B2
 KEGG 2 / 102 9.8× 1.75e-2 7.64e-2
Downregulation of ERBB4 signaling
ERBB4
 Reactome 1 / 9 55.6× 1.78e-2 7.75e-2
PI3K events in ERBB4 signaling
ERBB4
 Reactome 1 / 10 50.0× 1.98e-2 8.24e-2
Digestion of dietary carbohydrate
AMY1C
 Reactome 1 / 10 50.0× 1.98e-2 8.24e-2
Signaling by ERBB4
ERBB4
 Reactome 1 / 11 45.5× 2.18e-2 8.74e-2
Formation of annular gap junctions
ACTG1
 Reactome 1 / 11 45.5× 2.18e-2 8.74e-2
Cell-extracellular matrix interactions
ACTG1
 Reactome 1 / 12 41.7× 2.37e-2 9.18e-2
Gap junction degradation
ACTG1
 Reactome 1 / 12 41.7× 2.37e-2 9.18e-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 sound
COL11A1, RIPOR2, ATP2B2, WFS1
 GO:0007605 4 / 162 19.2× 5.05e-5 1.75e-3 ✓ sig.
olfactory behavior
LMX1A, WFS1
 GO:0042048 2 / 9 173× 5.66e-5 1.89e-3 ✓ sig.
phospholipid translocation
ATP11A, ABCC1
 GO:0045332 2 / 27 57.7× 5.44e-4 9.56e-3 ✓ sig.
host-mediated perturbation of viral transcription
PSMC3
 GO:0043921 1 / 1 779× 1.28e-3 1.61e-2 ✓ sig.
negative regulation of establishment of T cell polarity
RIPOR2
 GO:1903904 1 / 1 779× 1.28e-3 1.61e-2 ✓ sig.
negative regulation of protein localization to cell leading edge
RIPOR2
 GO:1905872 1 / 1 779× 1.28e-3 1.61e-2 ✓ sig.
cyclic nucleotide transport
ABCC1
 GO:0070729 1 / 1 779× 1.28e-3 1.61e-2 ✓ sig.
vestibular receptor cell stereocilium organization
PLS1
 GO:0060121 1 / 1 779× 1.28e-3 1.61e-2 ✓ sig.
succinyl-CoA pathway
SUCLA2
 GO:0006781 1 / 1 779× 1.28e-3 1.61e-2 ✓ sig.
negative regulation of cell adhesion
RIPOR2, CD164
 GO:0007162 2 / 49 31.8× 1.79e-3 1.93e-2 ✓ sig.
sphingolipid translocation
ABCC1
 GO:0099039 1 / 2 389× 2.57e-3 2.34e-2 ✓ sig.
central nervous system morphogenesis
ERBB4
 GO:0021551 1 / 2 389× 2.57e-3 2.34e-2 ✓ sig.
establishment of planar polarity involved in nephron morphogenesis
ERBB4
 GO:0072046 1 / 2 389× 2.57e-3 2.34e-2 ✓ sig.
negative regulation of Rho guanyl-nucleotide exchange factor activity
RIPOR2
 GO:2001107 1 / 2 389× 2.57e-3 2.34e-2 ✓ sig.
negative regulation of ATF6-mediated unfolded protein response
WFS1
 GO:1903892 1 / 2 389× 2.57e-3 2.34e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness, autosomal dominant 37 Fibrochondrogenesis 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Deafness, autosomal dominant 37 Fibrochondrogenesis 1 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Fibrochondrogenesis Fibrochondrogenesis 1 0.500 1 6.46e-5 1.99e-4 ✓ sig.
Intervertebral disc displacement Spondyloepiphyseal dysplasia with congenital joint dislocations 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Deafness, autosomal dominant 37 Intervertebral disc displacement 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Fibrochondrogenesis 1 Intervertebral disc displacement 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Fibrochondrogenesis Intervertebral disc displacement 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Mitochondrial dna depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria) Peritoneal disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Fibrochondrogenesis 1 Peritoneal disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Deafness, autosomal dominant 37 Peritoneal disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Fibrochondrogenesis Peritoneal disease 0.100 1 5.81e-4 1.00e-3 ✓ sig.
Autosomal dominant nonsyndromic hearing loss Deafness, autosomal dominant 7 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Autosomal dominant nonsyndromic hearing loss Deafness, autosomal dominant, 77 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Autosomal dominant nonsyndromic hearing loss Fibrochondrogenesis 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Autosomal dominant nonsyndromic hearing loss Deafness, autosomal dominant 21 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Autosomal dominant nonsyndromic hearing loss Fibrochondrogenesis 1 0.077 1 7.75e-4 1.25e-3 ✓ sig.
Autosomal dominant nonsyndromic hearing loss Deafness, autosomal dominant 37 0.077 1 7.75e-4 1.25e-3 ✓ sig.