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 257

8 diseases · 16 shared-gene connections
8 Diseases
29 Unique genes
0.199 Avg. similarity score
Peroxisome biogenesis disorder Most-connected disease (6 links)
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Disease Searched: Dilated cardiomyopathy 2B 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 ⇵
Peroxisome biogenesis disorder 6 6 24
Heimler syndrome 5 5 4
Refsum disease 5 5 6
Zellweger spectrum disorder 5 5 13
Adrenoleukodystrophy 4 4 6
Autosomal recessive ataxia 4 4 5
Dilated cardiomyopathy 2B 2 2 1
Arthrogryposis multiplex congenita 3, myogenic type 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
PEX1 5 / 8 Adrenoleukodystrophy, Heimler syndrome, Peroxisome biogenesis disorder, Refsum disease and 1 more
PEX26 5 / 8 Adrenoleukodystrophy, Heimler syndrome, Peroxisome biogenesis disorder, Refsum disease and 1 more
PEX2 4 / 8 Autosomal recessive ataxia, Peroxisome biogenesis disorder, Refsum disease, Zellweger spectrum disorder
PEX5 4 / 8 Adrenoleukodystrophy, Peroxisome biogenesis disorder, Refsum disease, Zellweger spectrum disorder
GATAD1 3 / 8 Dilated cardiomyopathy 2B, Heimler syndrome, Peroxisome biogenesis disorder
PEX10 3 / 8 Autosomal recessive ataxia, Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX16 3 / 8 Autosomal recessive ataxia, Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX6 3 / 8 Heimler syndrome, Peroxisome biogenesis disorder, Zellweger spectrum disorder
ABCD1 2 / 8 Adrenoleukodystrophy, Peroxisome biogenesis disorder
PEX11B 2 / 8 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX12 2 / 8 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX13 2 / 8 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX14 2 / 8 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX19 2 / 8 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX3 2 / 8 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX7 2 / 8 Peroxisome biogenesis disorder, Refsum disease
SYNE1 2 / 8 Arthrogryposis multiplex congenita 3, myogenic type, Autosomal recessive ataxia
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 ⇵
Peroxisome
ABCD1, PEX7, PHYH, PEX10, PEX16, PEX2, PEX1, PEX26, PEX6, PEX11B, PEX12, PEX13
 KEGG 19 / 83 94.8× 1.85e-35 1.01e-31 ✓ sig.
Class I peroxisomal membrane protein import
ABCD1, PEX16, PEX2, PEX26, PEX11B, PEX12, PEX13, PEX14, PEX19, PEX3
 Reactome 10 / 20 207× 2.13e-22 2.16e-19 ✓ sig.
Peroxisomal protein import
PEX7, PHYH, PEX10, PEX2, PEX1, PEX26, PEX6, PEX12, PEX13, PEX14, PEX5, ACOX1
 Reactome 12 / 63 78.9× 6.93e-21 5.60e-18 ✓ sig.
E3 ubiquitin ligases ubiquitinate target proteins
PEX10, PEX2, PEX12, PEX13, PEX14, PEX5, PAF1
 Reactome 7 / 59 49.1× 6.86e-11 7.96e-9 ✓ sig.
ABC transporters in lipid homeostasis
ABCD1, PEX19, PEX3
 Reactome 3 / 18 69.0× 1.01e-5 2.73e-4 ✓ sig.
Beta-oxidation of very long chain fatty acids
ABCD1, ACOX1
 Reactome 2 / 11 75.3× 3.05e-4 4.28e-3 ✓ sig.
alpha-linolenic acid (ALA) metabolism
ABCD1, ACOX1
 Reactome 2 / 13 63.7× 4.32e-4 5.62e-3 ✓ sig.
Biosynthesis of unsaturated fatty acids
SCD, ACOX1
 KEGG 2 / 27 30.7× 1.90e-3 1.76e-2 ✓ sig.
Defective ABCD1 causes adrenoleukodystrophy (ALD)
ABCD1
 Reactome 1 / 1 414× 2.41e-3 2.09e-2 ✓ sig.
Propanoate metabolism
MMUT, ACOX1
 KEGG 2 / 32 25.9× 2.67e-3 2.25e-2 ✓ sig.
Defective MMAA causes methylmalonic aciduria type cblA
MMUT
 Reactome 1 / 2 207× 4.82e-3 3.42e-2 ✓ sig.
Defective MUT causes methylmalonic aciduria mut type
MMUT
 Reactome 1 / 2 207× 4.82e-3 3.42e-2 ✓ sig.
Fatty acid metabolism
SCD, ACOX1
 KEGG 2 / 57 14.5× 8.28e-3 4.87e-2 ✓ sig.
Propionyl-CoA catabolism
MMUT
 Reactome 1 / 5 82.8× 1.20e-2 6.14e-2
PPAR signaling pathway
SCD, ACOX1
 KEGG 2 / 76 10.9× 1.44e-2 6.87e-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 ⇵
peroxisome organization
ABCD1, PEX7, PEX10, PEX16, PEX2, PEX1, PEX6, PEX11B, PEX12, PEX14, PEX19, PEX3
 GO:0007031 14 / 23 392× 8.71e-36 7.89e-32 ✓ sig.
protein import into peroxisome matrix
PEX7, PEX10, PEX16, PEX2, PEX1, PEX26, PEX6, PEX12, PEX13, PEX14, PEX5
 GO:0016558 11 / 14 506× 5.18e-30 3.16e-26 ✓ sig.
protein import into peroxisome matrix, receptor recycling
PEX10, PEX2, PEX1, PEX26, PEX6, PEX12, PEX13, PEX14, PEX5
 GO:0016562 9 / 10 580× 1.31e-25 4.77e-22 ✓ sig.
protein unfolding
PEX10, PEX2, PEX1, PEX26, PEX6, PEX12, PEX13, PEX14, PEX5
 GO:0043335 9 / 12 483× 2.87e-24 8.55e-21 ✓ sig.
protein targeting to peroxisome
PEX7, PEX16, PEX1, PEX6, PEX12, PEX19, PEX5
 GO:0006625 7 / 10 451× 1.18e-18 1.59e-15 ✓ sig.
protein import into peroxisome matrix, substrate release
PEX10, PEX2, PEX12, PEX13, PEX14, PEX5
 GO:0044721 6 / 6 644× 8.04e-18 9.55e-15 ✓ sig.
protein import into peroxisome membrane
PEX16, PEX26, PEX19, PEX3, PEX5
 GO:0045046 5 / 6 537× 3.75e-14 2.33e-11 ✓ sig.
protein import into peroxisome matrix, translocation
PEX6, PEX13, PEX14, PEX5
 GO:0016561 4 / 4 644× 4.68e-12 1.95e-9 ✓ sig.
peroxisome fission
PEX11B, PEX19, PEX11A, PEX11G, ACOX1
 GO:0016559 5 / 12 268× 4.92e-12 2.02e-9 ✓ sig.
cellular response to reactive oxygen species
PEX10, PEX2, PEX12, PEX13, PEX14, PEX5
 GO:0034614 6 / 45 85.9× 6.28e-11 2.02e-8 ✓ sig.
protein monoubiquitination
PEX10, PEX2, PEX12, PEX13, PEX14, PEX5
 GO:0006513 6 / 55 70.3× 2.21e-10 6.19e-8 ✓ sig.
peroxisome membrane biogenesis
PEX16, PEX19, PEX11A
 GO:0016557 3 / 3 644× 3.36e-9 6.77e-7 ✓ sig.
regulation of peroxisome size
PEX11B, PEX11A, PEX11G
 GO:0044375 3 / 3 644× 3.36e-9 6.77e-7 ✓ sig.
fatty acid beta-oxidation
ABCD1, PEX7, PEX2, PEX5, ACOX1
 GO:0006635 5 / 48 67.1× 1.02e-8 1.79e-6 ✓ sig.
protein import into peroxisome matrix, docking
PEX13, PEX14, PEX5
 GO:0016560 3 / 4 483× 1.34e-8 2.29e-6 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Peroxisome biogenesis disorder Zellweger spectrum disorder 0.520 13 5.29e-39 1.22e-37 ✓ sig.
Peroxisome biogenesis disorder Refsum disease 0.192 5 3.43e-14 3.99e-13 ✓ sig.
Heimler syndrome Peroxisome biogenesis disorder 0.160 4 4.43e-12 4.58e-11 ✓ sig.
Refsum disease Zellweger spectrum disorder 0.250 4 4.47e-12 4.61e-11 ✓ sig.
Adrenoleukodystrophy Peroxisome biogenesis disorder 0.148 4 6.64e-11 6.29e-10 ✓ sig.
Adrenoleukodystrophy Refsum disease 0.300 3 6.46e-10 5.67e-9 ✓ sig.
Heimler syndrome Zellweger spectrum disorder 0.200 3 1.85e-9 1.56e-8 ✓ sig.
Autosomal recessive ataxia Zellweger spectrum disorder 0.188 3 4.62e-9 3.79e-8 ✓ sig.
Adrenoleukodystrophy Zellweger spectrum disorder 0.176 3 9.23e-9 7.27e-8 ✓ sig.
Autosomal recessive ataxia Peroxisome biogenesis disorder 0.111 3 3.26e-8 2.43e-7 ✓ sig.
Adrenoleukodystrophy Heimler syndrome 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Heimler syndrome Refsum disease 0.222 2 7.50e-7 4.63e-6 ✓ sig.
Dilated cardiomyopathy 2B Heimler syndrome 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Arthrogryposis multiplex congenita 3, myogenic type Autosomal recessive ataxia 0.167 1 3.23e-4 6.41e-4 ✓ sig.
Dilated cardiomyopathy 2B Peroxisome biogenesis disorder 0.040 1 1.55e-3 2.19e-3 ✓ sig.
Autosomal recessive ataxia Refsum disease 0.091 1 1.94e-3 2.65e-3 ✓ sig.