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 99

11 diseases · 23 shared-gene connections
11 Diseases
15 Unique genes
0.257 Avg. similarity score
Bifunctional enzyme deficiency Most-connected disease (6 links)
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Disease Searched: Fanconi syndrome 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 ⇵
Bifunctional enzyme deficiency 6 6 2
De toni-debre-fanconi syndrome 6 6 4
Fanconi renotubular syndrome 6 6 4
Fanconi syndrome 6 6 6
Agat deficiency 4 4 1
Arginine-glycine amidinotransferase deficiency 4 4 1
Fatty acid metabolism disorder 4 4 3
D-bifunctional protein deficiency 3 3 1
Dominant hypophosphatemia with nephrolithiasis and/or osteoporosis 3 3 2
Peroxisomal disorder 3 3 4
Carnitine palmitoyltransferase deficiency 1 1 3

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

Gene ⇵ Member diseases ⇵ Linked diseases
GATM 5 / 11 Agat deficiency, Arginine-glycine amidinotransferase deficiency, De toni-debre-fanconi syndrome, Fanconi renotubular syndrome and 1 more
EHHADH 4 / 11 Bifunctional enzyme deficiency, De toni-debre-fanconi syndrome, Fanconi renotubular syndrome, Fanconi syndrome
HSD17B4 4 / 11 Bifunctional enzyme deficiency, D-bifunctional protein deficiency, Fatty acid metabolism disorder, Peroxisomal disorder
SLC34A1 4 / 11 De toni-debre-fanconi syndrome, Dominant hypophosphatemia with nephrolithiasis and/or osteoporosis, Fanconi renotubular syndrome, Fanconi syndrome
NDUFAF6 3 / 11 De toni-debre-fanconi syndrome, Fanconi renotubular syndrome, Fanconi syndrome
CPT1A 2 / 11 Carnitine palmitoyltransferase deficiency, Fatty acid metabolism disorder
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 ⇵
Fatty acid metabolism
EHHADH, HSD17B4, CPT1A, CPT2, CPT1B
 KEGG 5 / 57 70.2× 5.83e-9 5.77e-7 ✓ sig.
Peroxisomal protein import
EHHADH, HSD17B4, PEX1, PHYH, PIPOX
 Reactome 5 / 63 63.5× 9.74e-9 8.92e-7 ✓ sig.
Peroxisome
EHHADH, HSD17B4, PEX1, PHYH, PIPOX
 KEGG 5 / 83 48.2× 3.97e-8 3.07e-6 ✓ sig.
Fatty acid degradation
EHHADH, CPT1A, CPT2, CPT1B
 KEGG 4 / 43 74.5× 1.89e-7 1.22e-5 ✓ sig.
Carnitine metabolism
CPT1A, CPT2, CPT1B
 Reactome 3 / 14 172× 5.69e-7 3.17e-5 ✓ sig.
PPAR signaling pathway
EHHADH, CPT1A, CPT2, CPT1B
 KEGG 4 / 76 42.1× 1.92e-6 9.14e-5 ✓ sig.
Beta-oxidation of very long chain fatty acids
EHHADH, HSD17B4
 Reactome 2 / 11 146× 7.96e-5 1.94e-3 ✓ sig.
Thermogenesis
CPT1A, CPT2, NDUFAF6, CPT1B
 KEGG 4 / 234 13.7× 1.62e-4 3.40e-3 ✓ sig.
Glucagon signaling pathway
CPT1A, CPT1B, SLC2A2
 KEGG 3 / 107 22.4× 2.89e-4 5.37e-3 ✓ sig.
Signaling by Retinoic Acid
CPT1A, CPT1B
 Reactome 2 / 21 76.3× 3.02e-4 5.55e-3 ✓ sig.
Insulin resistance
CPT1A, CPT1B, SLC2A2
 KEGG 3 / 109 22.0× 3.06e-4 5.61e-3 ✓ sig.
Glycine, serine and threonine metabolism
GATM, PIPOX
 KEGG 2 / 40 40.0× 1.10e-3 1.52e-2 ✓ sig.
Defective SLC2A2 causes Fanconi-Bickel syndrome (FBS)
SLC2A2
 Reactome 1 / 1 801× 1.25e-3 1.66e-2 ✓ sig.
Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1)
SLC34A1
 Reactome 1 / 1 801× 1.25e-3 1.66e-2 ✓ sig.
Lysine degradation
EHHADH, PIPOX
 KEGG 2 / 63 25.4× 2.72e-3 2.95e-2 ✓ sig.

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

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
fatty acid beta-oxidation
EHHADH, HSD17B4, CPT1A, CPT2, CPT1B
 GO:0006635 5 / 48 130× 2.66e-10 6.95e-8 ✓ sig.
carnitine shuttle
CPT1A, CPT2, CPT1B
 GO:0006853 3 / 4 934× 1.67e-9 3.56e-7 ✓ sig.
fatty acid metabolic process
EHHADH, HSD17B4, CPT1A, CPT2, CPT1B, PHYH
 GO:0006631 6 / 211 35.4× 8.87e-9 1.53e-6 ✓ sig.
carnitine metabolic process
CPT1A, CPT2, CPT1B
 GO:0009437 3 / 8 467× 2.34e-8 3.58e-6 ✓ sig.
fatty acid derivative biosynthetic process
EHHADH, HSD17B4
 GO:1901570 2 / 12 208× 3.95e-5 1.56e-3 ✓ sig.
fatty acid beta-oxidation using acyl-CoA oxidase
EHHADH, HSD17B4
 GO:0033540 2 / 14 178× 5.44e-5 1.98e-3 ✓ sig.
alpha-linolenic acid metabolic process
EHHADH, HSD17B4
 GO:0036109 2 / 16 156× 7.17e-5 2.44e-3 ✓ sig.
unsaturated fatty acid biosynthetic process
EHHADH, HSD17B4
 GO:0006636 2 / 24 104× 1.64e-4 4.52e-3 ✓ sig.
long-chain fatty acid metabolic process
CPT1A, CPT2
 GO:0001676 2 / 29 85.9× 2.41e-4 5.95e-3 ✓ sig.
long-chain fatty acid biosynthetic process
EHHADH, HSD17B4
 GO:0042759 2 / 33 75.5× 3.13e-4 7.18e-3 ✓ sig.
lipid metabolic process
EHHADH, HSD17B4, CPT1A, CPT2, CPT1B
 GO:0006629 5 / 840 7.4× 3.73e-4 8.08e-3 ✓ sig.
indole metabolic process
SLC34A1
 GO:0042431 1 / 1 1,246× 8.03e-4 1.35e-2 ✓ sig.
gentamycin metabolic process
SLC34A1
 GO:1901128 1 / 1 1,246× 8.03e-4 1.35e-2 ✓ sig.
arsenate ion transmembrane transport
SLC34A1
 GO:1901684 1 / 1 1,246× 8.03e-4 1.35e-2 ✓ sig.
positive regulation of phosphate transmembrane transport
SLC34A1
 GO:2000187 1 / 1 1,246× 8.03e-4 1.35e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
De toni-debre-fanconi syndrome Fanconi renotubular syndrome 0.800 4 4.27e-16 6.52e-15 ✓ sig.
De toni-debre-fanconi syndrome Fanconi syndrome 0.571 4 6.41e-15 9.10e-14 ✓ sig.
Fanconi renotubular syndrome Fanconi syndrome 0.571 4 6.41e-15 9.10e-14 ✓ sig.
Agat deficiency Arginine-glycine amidinotransferase deficiency 0.500 1 6.49e-5 2.33e-4 ✓ sig.
Bifunctional enzyme deficiency D-bifunctional protein deficiency 0.333 1 1.30e-4 3.93e-4 ✓ sig.
D-bifunctional protein deficiency Fatty acid metabolism disorder 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Agat deficiency De toni-debre-fanconi syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
D-bifunctional protein deficiency Peroxisomal disorder 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Arginine-glycine amidinotransferase deficiency Fanconi renotubular syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Arginine-glycine amidinotransferase deficiency De toni-debre-fanconi syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Agat deficiency Fanconi renotubular syndrome 0.200 1 2.60e-4 6.51e-4 ✓ sig.
Bifunctional enzyme deficiency Fatty acid metabolism disorder 0.200 1 3.90e-4 8.67e-4 ✓ sig.
Arginine-glycine amidinotransferase deficiency Fanconi syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Agat deficiency Fanconi syndrome 0.143 1 3.90e-4 8.67e-4 ✓ sig.
Dominant hypophosphatemia with nephrolithiasis and/or osteoporosis Fanconi renotubular syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
De toni-debre-fanconi syndrome Dominant hypophosphatemia with nephrolithiasis and/or osteoporosis 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Bifunctional enzyme deficiency Peroxisomal disorder 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Bifunctional enzyme deficiency Fanconi renotubular syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Bifunctional enzyme deficiency De toni-debre-fanconi syndrome 0.167 1 5.19e-4 1.06e-3 ✓ sig.
Carnitine palmitoyltransferase deficiency Fatty acid metabolism disorder 0.167 1 5.84e-4 1.16e-3 ✓ sig.
Fatty acid metabolism disorder Peroxisomal disorder 0.143 1 7.79e-4 1.41e-3 ✓ sig.
Dominant hypophosphatemia with nephrolithiasis and/or osteoporosis Fanconi syndrome 0.125 1 7.79e-4 1.41e-3 ✓ sig.
Bifunctional enzyme deficiency Fanconi syndrome 0.125 1 7.79e-4 1.41e-3 ✓ sig.