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 219

8 diseases · 14 shared-gene connections
8 Diseases
7 Unique genes
0.295 Avg. similarity score
Deafness enamel hypoplasia nail defects Most-connected disease (5 links)
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Disease Searched: Central nervous system demyelinating 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 ⇵
Deafness enamel hypoplasia nail defects 5 5 2
Deafness-enamel hypoplasia-nail defects syndrome 5 5 2
Heimler syndrome 5 5 4
Central nervous system demyelinating disease 4 4 4
Spinocerebellar ataxia blindness deafness syndrome 4 4 1
peroxisome biogenesis disorder due to PEX1 defect 3 3 1
dilated cardiomyopathy 2B 1 1 1
megalencephalic leukoencephalopathy with subcortical cysts 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PEX6 5 / 8 Central nervous system demyelinating disease, Deafness enamel hypoplasia nail defects, Deafness-enamel hypoplasia-nail defects syndrome, Heimler syndrome and 1 more
PEX1 4 / 8 Deafness enamel hypoplasia nail defects, Deafness-enamel hypoplasia-nail defects syndrome, Heimler syndrome, peroxisome biogenesis disorder due to PEX1 defect
GATAD1 2 / 8 dilated cardiomyopathy 2B, Heimler syndrome
MLC1 2 / 8 Central nervous system demyelinating disease, megalencephalic leukoencephalopathy with subcortical cysts 1
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 ⇵
Peroxisomal protein import
PEX6, PEX1, PEX26
 Reactome 3 / 63 81.7× 4.74e-6 1.94e-4 ✓ sig.
Peroxisome
PEX6, PEX1, PEX26
 KEGG 3 / 83 62.0× 1.09e-5 3.82e-4 ✓ sig.
Mitochondrial tRNA aminoacylation
DARS2
 Reactome 1 / 14 123× 8.13e-3 6.22e-2
Class I peroxisomal membrane protein import
PEX26
 Reactome 1 / 20 85.8× 1.16e-2 7.77e-2
Mineral absorption
CLCN2
 KEGG 1 / 61 28.1× 3.50e-2 1.46e-1
Aminoacyl-tRNA biosynthesis
DARS2
 KEGG 1 / 66 26.0× 3.78e-2 1.52e-1
Stimuli-sensing channels
CLCN2
 Reactome 1 / 79 21.7× 4.52e-2 1.67e-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 ⇵
protein import into peroxisome matrix, receptor recycling
PEX6, PEX1, PEX26
 GO:0016562 3 / 10 801× 3.86e-9 7.38e-7 ✓ sig.
protein unfolding
PEX6, PEX1, PEX26
 GO:0043335 3 / 12 667× 7.07e-9 1.25e-6 ✓ sig.
protein import into peroxisome matrix
PEX6, PEX1, PEX26
 GO:0016558 3 / 14 572× 1.17e-8 1.95e-6 ✓ sig.
protein targeting to peroxisome
PEX6, PEX1
 GO:0006625 2 / 10 534× 5.40e-6 3.31e-4 ✓ sig.
peroxisome organization
PEX6, PEX1
 GO:0007031 2 / 23 232× 3.03e-5 1.27e-3 ✓ sig.
mitochondrial asparaginyl-tRNA aminoacylation
DARS2
 GO:0070145 1 / 1 2,670× 3.75e-4 8.08e-3 ✓ sig.
regulation of aldosterone biosynthetic process
CLCN2
 GO:0032347 1 / 1 2,670× 3.75e-4 8.08e-3 ✓ sig.
aspartyl-tRNA aminoacylation
DARS2
 GO:0006422 1 / 2 1,335× 7.49e-4 1.30e-2 ✓ sig.
cell differentiation involved in salivary gland development
CLCN2
 GO:0060689 1 / 2 1,335× 7.49e-4 1.30e-2 ✓ sig.
regulation of response to osmotic stress
MLC1
 GO:0047484 1 / 2 1,335× 7.49e-4 1.30e-2 ✓ sig.
regulation of membrane depolarization during action potential
CLCN2
 GO:0098902 1 / 2 1,335× 7.49e-4 1.30e-2 ✓ sig.
microtubule-based peroxisome localization
PEX1
 GO:0060152 1 / 2 1,335× 7.49e-4 1.30e-2 ✓ sig.
stabilization of membrane potential
CLCN2
 GO:0030322 1 / 3 890× 1.12e-3 1.68e-2 ✓ sig.
protein transport
MLC1, PEX1, PEX26
 GO:0015031 3 / 667 12.0× 1.42e-3 1.93e-2 ✓ sig.
protein import into peroxisome matrix, translocation
PEX6
 GO:0016561 1 / 4 667× 1.50e-3 1.98e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Deafness enamel hypoplasia nail defects Deafness-enamel hypoplasia-nail defects syndrome 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Deafness enamel hypoplasia nail defects Heimler syndrome 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome Heimler syndrome 0.400 2 5.06e-8 3.71e-7 ✓ sig.
Deafness enamel hypoplasia nail defects Spinocerebellar ataxia blindness deafness syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Deafness enamel hypoplasia nail defects peroxisome biogenesis disorder due to PEX1 defect 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome Spinocerebellar ataxia blindness deafness syndrome 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome peroxisome biogenesis disorder due to PEX1 defect 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Central nervous system demyelinating disease Spinocerebellar ataxia blindness deafness syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Central nervous system demyelinating disease megalencephalic leukoencephalopathy with subcortical cysts 1 0.200 1 2.60e-4 6.51e-4 ✓ sig.
dilated cardiomyopathy 2B Heimler syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Heimler syndrome Spinocerebellar ataxia blindness deafness syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Heimler syndrome peroxisome biogenesis disorder due to PEX1 defect 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Central nervous system demyelinating disease Deafness enamel hypoplasia nail defects 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Central nervous system demyelinating disease Deafness-enamel hypoplasia-nail defects syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.