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 74

13 diseases · 18 shared-gene connections
13 Diseases
36 Unique genes
0.119 Avg. similarity score
Amino acid metabolism disorder Most-connected disease (8 links)
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Disease Searched: lysinuric protein intolerance 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 ⇵
Amino acid metabolism disorder 8 8 26
Urea cycle disorder 7 7 8
Citrullinemia 4 4 3
Hyperammonemia 3 3 8
ornithine translocase deficiency 3 3 1
Argininosuccinic aciduria 2 2 1
Citrin deficiency 2 2 1
ornithine carbamoyltransferase deficiency 2 2 1
Cystathioninuria 1 1 1
Hyperprolinemia 1 1 2
lysinuric protein intolerance 1 1 1
propionic acidemia 1 1 2
systemic lupus erythematosus, susceptibility to, 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
SLC25A15 4 / 13 Amino acid metabolism disorder, Citrullinemia, ornithine translocase deficiency, Urea cycle disorder
ASL 3 / 13 Amino acid metabolism disorder, Argininosuccinic aciduria, Urea cycle disorder
NAGS 3 / 13 Amino acid metabolism disorder, Hyperammonemia, Urea cycle disorder
OTC 3 / 13 Hyperammonemia, ornithine carbamoyltransferase deficiency, Urea cycle disorder
SLC25A13 3 / 13 Citrin deficiency, Citrullinemia, Urea cycle disorder
ARG1 2 / 13 Amino acid metabolism disorder, Urea cycle disorder
ASS1 2 / 13 Citrullinemia, Urea cycle disorder
CPS1 2 / 13 Hyperammonemia, Urea cycle disorder
CTH 2 / 13 Amino acid metabolism disorder, Cystathioninuria
PCCA 2 / 13 Amino acid metabolism disorder, propionic acidemia
PCCB 2 / 13 Amino acid metabolism disorder, propionic acidemia
PRODH 2 / 13 Amino acid metabolism disorder, Hyperprolinemia
SLC7A7 2 / 13 Amino acid metabolism disorder, lysinuric protein intolerance
TLR5 2 / 13 Hyperammonemia, systemic lupus erythematosus, susceptibility to, 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 ⇵
Urea cycle
ASS1, ARG1, ASL, NAGS, SLC25A15, CPS1, OTC
 Reactome 7 / 10 234× 1.39e-16 5.67e-14 ✓ sig.
Biosynthesis of amino acids
ASS1, ARG1, ASL, CTH, MAT1A, NAGS, PHGDH, PSPH, CPS1, OTC
 KEGG 10 / 75 44.5× 1.08e-14 3.05e-12 ✓ sig.
Arginine biosynthesis
ASS1, ARG1, ASL, NAGS, CPS1, OTC, GLUD1
 KEGG 7 / 23 102× 2.77e-13 6.01e-11 ✓ sig.
Metabolic pathways
ASS1, AHCY, ALDH6A1, ARG1, ASL, CTH, GAMT, GCLC, HMGCL, IVD, MAT1A, NAGS
 KEGG 22 / 1,563 4.7× 1.75e-11 2.78e-9 ✓ sig.
Carbon metabolism
ALDH6A1, PCCA, PCCB, PHGDH, PSPH, CPS1, GLUD1
 KEGG 7 / 115 20.3× 4.07e-8 2.86e-6 ✓ sig.
Alanine, aspartate and glutamate metabolism
ASS1, ASL, CPS1, GLUD1, ALDH4A1
 KEGG 5 / 37 45.1× 7.37e-8 4.85e-6 ✓ sig.
Valine, leucine and isoleucine degradation
ALDH6A1, HMGCL, IVD, PCCA, PCCB
 KEGG 5 / 48 34.8× 2.83e-7 1.56e-5 ✓ sig.
Cysteine and methionine metabolism
AHCY, CTH, GCLC, MAT1A, PHGDH
 KEGG 5 / 52 32.1× 4.26e-7 2.23e-5 ✓ sig.
One carbon pool by folate
AHCY, CTH, MAT1A, TYMS
 KEGG 4 / 38 35.1× 4.67e-6 1.74e-4 ✓ sig.
Glycine, serine and threonine metabolism
CTH, GAMT, PHGDH, PSPH
 KEGG 4 / 40 33.4× 5.75e-6 2.06e-4 ✓ sig.
Arginine and proline metabolism
ARG1, GAMT, PRODH, ALDH4A1
 KEGG 4 / 50 26.7× 1.42e-5 4.36e-4 ✓ sig.
Proline catabolism
PRODH, ALDH4A1
 Reactome 2 / 3 222× 2.62e-5 7.32e-4 ✓ sig.
Propionyl-CoA catabolism
PCCA, PCCB
 Reactome 2 / 5 133× 8.69e-5 1.95e-3 ✓ sig.
Propanoate metabolism
ALDH6A1, PCCA, PCCB
 KEGG 3 / 32 31.3× 1.16e-4 2.45e-3 ✓ sig.
Sulfur amino acid metabolism
AHCY, MAT1A
 Reactome 2 / 6 111× 1.30e-4 2.70e-3 ✓ 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 ⇵
urea cycle
ASS1, ARG1, ASL, NAGS, SLC25A15, CPS1, OTC
 GO:0000050 7 / 12 303× 4.16e-17 4.17e-14 ✓ sig.
amino acid biosynthetic process
ASS1, ASL, CTH, PHGDH, PSPH, OTC
 GO:0008652 6 / 27 115× 9.48e-12 3.50e-9 ✓ sig.
L-arginine biosynthetic process
ASS1, ASL, NAGS, OTC
 GO:0006526 4 / 4 519× 1.16e-11 4.21e-9 ✓ sig.
response to zinc ion
ASS1, D2HGDH, CPS1, OTC
 GO:0010043 4 / 27 76.9× 1.97e-7 2.13e-5 ✓ sig.
midgut development
ASS1, CPS1, OTC
 GO:0007494 3 / 8 195× 3.65e-7 3.57e-5 ✓ sig.
glutamine metabolic process
PHGDH, CPS1, GLUD1
 GO:0006541 3 / 15 104× 2.94e-6 1.97e-4 ✓ sig.
L-arginine biosynthetic process via ornithine
ASL, OTC
 GO:0042450 2 / 2 519× 3.61e-6 2.33e-4 ✓ sig.
monoatomic anion homeostasis
CPS1, OTC
 GO:0055081 2 / 2 519× 3.61e-6 2.33e-4 ✓ sig.
response to xenobiotic stimulus
ASS1, GCLC, XPC, CPS1, OTC, ABCA3
 GO:0009410 6 / 248 12.6× 7.18e-6 4.05e-4 ✓ sig.
proline metabolic process
PRODH, ALDH4A1
 GO:0006560 2 / 3 346× 1.08e-5 5.58e-4 ✓ sig.
L-proline catabolic process to L-glutamate
PRODH, ALDH4A1
 GO:0010133 2 / 3 346× 1.08e-5 5.58e-4 ✓ sig.
cellular response to oleic acid
ASS1, CPS1
 GO:0071400 2 / 3 346× 1.08e-5 5.58e-4 ✓ sig.
short-chain fatty acid catabolic process
PCCA, PCCB
 GO:0019626 2 / 3 346× 1.08e-5 5.58e-4 ✓ sig.
L-proline catabolic process
PRODH, ALDH4A1
 GO:0006562 2 / 4 260× 2.16e-5 9.60e-4 ✓ sig.
trans-4-hydroxy-L-proline catabolic process
PRODH, ALDH4A1
 GO:0019470 2 / 4 260× 2.16e-5 9.60e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Citrullinemia Urea cycle disorder 0.333 3 9.21e-11 9.15e-10 ✓ sig.
Amino acid metabolism disorder Urea cycle disorder 0.129 4 4.45e-10 4.17e-9 ✓ sig.
Hyperammonemia Urea cycle disorder 0.214 3 5.15e-9 4.34e-8 ✓ sig.
Amino acid metabolism disorder propionic acidemia 0.074 2 2.74e-6 1.49e-5 ✓ sig.
Citrin deficiency Citrullinemia 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Citrullinemia ornithine translocase deficiency 0.250 1 1.95e-4 5.35e-4 ✓ sig.
Argininosuccinic aciduria Urea cycle disorder 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Citrin deficiency Urea cycle disorder 0.111 1 5.20e-4 1.06e-3 ✓ sig.
ornithine translocase deficiency Urea cycle disorder 0.111 1 5.20e-4 1.06e-3 ✓ sig.
ornithine carbamoyltransferase deficiency Urea cycle disorder 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Hyperammonemia systemic lupus erythematosus, susceptibility to, 1 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Hyperammonemia ornithine carbamoyltransferase deficiency 0.111 1 5.20e-4 1.06e-3 ✓ sig.
Amino acid metabolism disorder ornithine translocase deficiency 0.037 1 1.69e-3 2.53e-3 ✓ sig.
Amino acid metabolism disorder lysinuric protein intolerance 0.037 1 1.69e-3 2.53e-3 ✓ sig.
Amino acid metabolism disorder Cystathioninuria 0.037 1 1.69e-3 2.53e-3 ✓ sig.
Amino acid metabolism disorder Argininosuccinic aciduria 0.037 1 1.69e-3 2.53e-3 ✓ sig.
Amino acid metabolism disorder Hyperprolinemia 0.036 1 3.37e-3 4.37e-3 ✓ sig.
Amino acid metabolism disorder Citrullinemia 0.034 1 5.06e-3 6.19e-3 ✓ sig.