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 202

8 diseases · 12 shared-gene connections
8 Diseases
13 Unique genes
0.152 Avg. similarity score
Hyperammonemia Most-connected disease (6 links)
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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 ⇵
Hyperammonemia 6 6 8
Urea cycle disorder 6 6 8
Congenital hyperammonemia 3 3 1
carbamoyl phosphate synthetase I deficiency disease 3 3 1
hyperammonemia due to N-acetylglutamate synthase deficiency 2 2 1
ornithine carbamoyltransferase deficiency 2 2 1
Argininosuccinic aciduria 1 1 1
systemic lupus erythematosus, susceptibility to, 1 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
CPS1 4 / 8 carbamoyl phosphate synthetase I deficiency disease, Congenital hyperammonemia, Hyperammonemia, Urea cycle disorder
NAGS 3 / 8 Hyperammonemia, hyperammonemia due to N-acetylglutamate synthase deficiency, Urea cycle disorder
OTC 3 / 8 Hyperammonemia, ornithine carbamoyltransferase deficiency, Urea cycle disorder
ASL 2 / 8 Argininosuccinic aciduria, Urea cycle disorder
TLR5 2 / 8 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
ASL, CPS1, ARG1, ASS1, NAGS, OTC, SLC25A15
 Reactome 7 / 10 647× 2.88e-20 2.31e-17 ✓ sig.
Arginine biosynthesis
ASL, CPS1, ARG1, ASS1, NAGS, OTC, GLUD1
 KEGG 7 / 23 281× 5.85e-17 2.77e-14 ✓ sig.
Biosynthesis of amino acids
ASL, CPS1, ARG1, ASS1, NAGS, OTC
 KEGG 6 / 75 73.9× 8.02e-11 1.18e-8 ✓ sig.
Alanine, aspartate and glutamate metabolism
ASL, CPS1, ASS1, GLUD1
 KEGG 4 / 37 99.9× 5.34e-8 3.78e-6 ✓ sig.
Metabolic pathways
ASL, CPS1, ARG1, ASS1, NAGS, OTC, GLUD1, TYMS
 KEGG 8 / 1,563 4.7× 5.67e-5 1.42e-3 ✓ sig.
Nitrogen metabolism
CPS1, GLUD1
 KEGG 2 / 17 109× 1.46e-4 3.04e-3 ✓ sig.
Defective ABCA3 causes pulmonary surfactant metabolism dysfunction type 3 (SMDP3)
ABCA3
 Reactome 1 / 1 924× 1.08e-3 1.44e-2 ✓ sig.
Defective ABCA3 causes pulmonary surfactant metabolism dysfunction 3 (SMDP3)
ABCA3
 Reactome 1 / 1 924× 1.08e-3 1.44e-2 ✓ sig.
Toll Like Receptor 5 (TLR5) Cascade
TLR5
 Reactome 1 / 1 924× 1.08e-3 1.44e-2 ✓ sig.
MyD88 deficiency (TLR5)
TLR5
 Reactome 1 / 2 462× 2.16e-3 2.42e-2 ✓ sig.
IRAK4 deficiency (TLR5)
TLR5
 Reactome 1 / 4 231× 4.32e-3 3.98e-2 ✓ sig.
Carbon metabolism
CPS1, GLUD1
 KEGG 2 / 115 16.1× 6.62e-3 5.28e-2
MyD88 cascade initiated on plasma membrane
TLR5
 Reactome 1 / 9 103× 9.70e-3 6.74e-2
Aspartate and asparagine metabolism
SLC25A13
 Reactome 1 / 12 77.0× 1.29e-2 7.95e-2
Glutamate and glutamine metabolism
GLUD1
 Reactome 1 / 14 66.0× 1.51e-2 8.71e-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 ⇵
urea cycle
ASL, CPS1, ARG1, ASS1, NAGS, OTC, SLC25A15
 GO:0000050 7 / 12 839× 8.61e-21 1.55e-17 ✓ sig.
L-arginine biosynthetic process
ASL, ASS1, NAGS, OTC
 GO:0006526 4 / 4 1,437× 1.41e-13 7.53e-11 ✓ sig.
midgut development
CPS1, ASS1, OTC
 GO:0007494 3 / 8 539× 1.47e-8 2.39e-6 ✓ sig.
L-arginine biosynthetic process via ornithine
ASL, OTC
 GO:0042450 2 / 2 1,437× 4.47e-7 4.25e-5 ✓ sig.
monoatomic anion homeostasis
CPS1, OTC
 GO:0055081 2 / 2 1,437× 4.47e-7 4.25e-5 ✓ sig.
amino acid biosynthetic process
ASL, ASS1, OTC
 GO:0008652 3 / 27 160× 7.62e-7 6.67e-5 ✓ sig.
response to zinc ion
CPS1, ASS1, OTC
 GO:0010043 3 / 27 160× 7.62e-7 6.67e-5 ✓ sig.
cellular response to oleic acid
CPS1, ASS1
 GO:0071400 2 / 3 958× 1.34e-6 1.04e-4 ✓ sig.
amino acid metabolic process
ASL, OTC, GLUD1
 GO:0006520 3 / 37 117× 2.02e-6 1.45e-4 ✓ sig.
citrulline biosynthetic process
CPS1, OTC
 GO:0019240 2 / 4 719× 2.68e-6 1.82e-4 ✓ sig.
positive regulation of nitric oxide biosynthetic process
ASL, ASS1, TLR5
 GO:0045429 3 / 42 103× 2.97e-6 1.98e-4 ✓ sig.
cellular response to ammonium ion
CPS1, ASS1
 GO:0071242 2 / 5 575× 4.46e-6 2.74e-4 ✓ sig.
response to glucocorticoid
CPS1, ASS1, ABCA3
 GO:0051384 3 / 53 81.4× 6.04e-6 3.49e-4 ✓ sig.
arginine metabolic process
ASL, ARG1
 GO:0006525 2 / 8 359× 1.25e-5 6.21e-4 ✓ sig.
response to xenobiotic stimulus
CPS1, ASS1, OTC, ABCA3
 GO:0009410 4 / 248 23.2× 1.97e-5 8.87e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hyperammonemia Urea cycle disorder 0.214 3 5.15e-9 4.60e-8 ✓ sig.
carbamoyl phosphate synthetase I deficiency disease Congenital hyperammonemia 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Argininosuccinic aciduria Urea cycle disorder 0.111 1 5.20e-4 1.04e-3 ✓ sig.
carbamoyl phosphate synthetase I deficiency disease Urea cycle disorder 0.111 1 5.20e-4 1.04e-3 ✓ sig.
carbamoyl phosphate synthetase I deficiency disease Hyperammonemia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Congenital hyperammonemia Urea cycle disorder 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Congenital hyperammonemia Hyperammonemia 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Hyperammonemia systemic lupus erythematosus, susceptibility to, 1 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Hyperammonemia hyperammonemia due to N-acetylglutamate synthase deficiency 0.111 1 5.20e-4 1.04e-3 ✓ sig.
hyperammonemia due to N-acetylglutamate synthase deficiency Urea cycle disorder 0.111 1 5.20e-4 1.04e-3 ✓ sig.
ornithine carbamoyltransferase deficiency Urea cycle disorder 0.111 1 5.20e-4 1.04e-3 ✓ sig.
Hyperammonemia ornithine carbamoyltransferase deficiency 0.111 1 5.20e-4 1.04e-3 ✓ sig.