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 112

11 diseases · 19 shared-gene connections
11 Diseases
28 Unique genes
0.219 Avg. similarity score
Amino acid metabolism disorder Most-connected disease (7 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 ⇵
Amino acid metabolism disorder 7 7 26
Hepatic methionine adenosyltransferase deficiency 6 6 3
S-adenosylhomocysteine hydrolase deficiency 6 6 3
Sulfur amino acid metabolism disorder 5 5 3
hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase 4 4 1
Glycine n-methyltransferase deficiency 3 3 1
methionine adenosyltransferase deficiency 3 3 1
Adenosine kinase deficiency 1 1 1
Cystathioninuria 1 1 1
lysinuric protein intolerance 1 1 1
propionic acidemia 1 1 2

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

Gene ⇵ Member diseases ⇵ Linked diseases
AHCY 5 / 11 Amino acid metabolism disorder, Hepatic methionine adenosyltransferase deficiency, hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase, S-adenosylhomocysteine hydrolase deficiency and 1 more
GNMT 4 / 11 Glycine n-methyltransferase deficiency, Hepatic methionine adenosyltransferase deficiency, S-adenosylhomocysteine hydrolase deficiency, Sulfur amino acid metabolism disorder
MAT1A 4 / 11 Amino acid metabolism disorder, Hepatic methionine adenosyltransferase deficiency, methionine adenosyltransferase deficiency, S-adenosylhomocysteine hydrolase deficiency
ADK 2 / 11 Adenosine kinase deficiency, Sulfur amino acid metabolism disorder
CTH 2 / 11 Amino acid metabolism disorder, Cystathioninuria
PCCA 2 / 11 Amino acid metabolism disorder, propionic acidemia
PCCB 2 / 11 Amino acid metabolism disorder, propionic acidemia
SLC7A7 2 / 11 Amino acid metabolism disorder, lysinuric protein intolerance
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 ⇵
Biosynthesis of amino acids
ARG1, ASL, CTH, MAT1A, NAGS, PHGDH, PSPH
 KEGG 7 / 75 40.0× 2.97e-10 3.84e-8 ✓ sig.
Metabolic pathways
ADK, AHCY, ALDH6A1, ARG1, ASL, CTH, GAMT, GCLC, HMGCL, IVD, MAT1A, NAGS
 KEGG 18 / 1,563 4.9× 3.77e-10 4.73e-8 ✓ sig.
Cysteine and methionine metabolism
AHCY, CTH, GCLC, MAT1A, PHGDH, GNMT
 KEGG 6 / 52 49.5× 1.71e-9 1.79e-7 ✓ sig.
Urea cycle
ARG1, ASL, NAGS, SLC25A15
 Reactome 4 / 10 172× 4.92e-9 4.67e-7 ✓ sig.
Glycine, serine and threonine metabolism
CTH, GAMT, PHGDH, PSPH, GNMT
 KEGG 5 / 40 53.6× 2.94e-8 2.26e-6 ✓ sig.
Valine, leucine and isoleucine degradation
ALDH6A1, HMGCL, IVD, PCCA, PCCB
 KEGG 5 / 48 44.7× 7.55e-8 5.10e-6 ✓ sig.
One carbon pool by folate
AHCY, CTH, MAT1A, GNMT
 KEGG 4 / 38 45.2× 1.65e-6 7.49e-5 ✓ sig.
Carbon metabolism
ALDH6A1, PCCA, PCCB, PHGDH, PSPH
 KEGG 5 / 115 18.6× 6.08e-6 2.21e-4 ✓ sig.
Arginine biosynthesis
ARG1, ASL, NAGS
 KEGG 3 / 23 55.9× 1.95e-5 5.86e-4 ✓ sig.
Propionyl-CoA catabolism
PCCA, PCCB
 Reactome 2 / 5 172× 5.22e-5 1.32e-3 ✓ sig.
Propanoate metabolism
ALDH6A1, PCCA, PCCB
 KEGG 3 / 32 40.2× 5.38e-5 1.36e-3 ✓ sig.
Sulfur amino acid metabolism
AHCY, MAT1A
 Reactome 2 / 6 143× 7.82e-5 1.83e-3 ✓ sig.
Defective HLCS causes multiple carboxylase deficiency
PCCA, PCCB
 Reactome 2 / 7 123× 1.09e-4 2.41e-3 ✓ sig.
Serine biosynthesis
PHGDH, PSPH
 Reactome 2 / 9 95.3× 1.87e-4 3.72e-3 ✓ sig.
Arginine and proline metabolism
ARG1, GAMT, PRODH
 KEGG 3 / 50 25.7× 2.07e-4 4.01e-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
ARG1, ASL, NAGS, SLC25A15
 GO:0000050 4 / 12 222× 1.98e-9 4.09e-7 ✓ sig.
amino acid biosynthetic process
ASL, CTH, PHGDH, PSPH
 GO:0008652 4 / 27 98.9× 6.91e-8 8.90e-6 ✓ sig.
one-carbon metabolic process
AHCY, MAT1A, GNMT
 GO:0006730 3 / 21 95.3× 3.94e-6 2.48e-4 ✓ sig.
short-chain fatty acid catabolic process
PCCA, PCCB
 GO:0019626 2 / 3 445× 6.49e-6 3.69e-4 ✓ sig.
L-arginine biosynthetic process
ASL, NAGS
 GO:0006526 2 / 4 334× 1.30e-5 6.40e-4 ✓ sig.
branched-chain amino acid metabolic process
PCCA, PCCB
 GO:0009081 2 / 5 267× 2.16e-5 9.54e-4 ✓ sig.
cysteine metabolic process
CTH, GCLC
 GO:0006534 2 / 6 222× 3.24e-5 1.29e-3 ✓ sig.
L-serine biosynthetic process
PHGDH, PSPH
 GO:0006564 2 / 6 222× 3.24e-5 1.29e-3 ✓ sig.
L-leucine catabolic process
HMGCL, IVD
 GO:0006552 2 / 7 191× 4.53e-5 1.67e-3 ✓ sig.
arginine metabolic process
ARG1, ASL
 GO:0006525 2 / 8 167× 6.03e-5 2.06e-3 ✓ sig.
L-serine metabolic process
PHGDH, PSPH
 GO:0006563 2 / 10 133× 9.67e-5 2.95e-3 ✓ sig.
protein homotetramerization
CTH, MAT1A, GNMT
 GO:0051289 3 / 66 30.3× 1.29e-4 3.67e-3 ✓ sig.
L-arginine transmembrane transport
SLC25A15, SLC7A7
 GO:1903826 2 / 15 89.0× 2.25e-4 5.47e-3 ✓ sig.
glutamate metabolic process
GCLC, NAGS
 GO:0006536 2 / 15 89.0× 2.25e-4 5.47e-3 ✓ sig.
branched-chain amino acid catabolic process
ALDH6A1, IVD
 GO:0009083 2 / 18 74.2× 3.26e-4 7.11e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hepatic methionine adenosyltransferase deficiency S-adenosylhomocysteine hydrolase deficiency 0.750 3 1.64e-12 2.04e-11 ✓ sig.
Hepatic methionine adenosyltransferase deficiency Sulfur amino acid metabolism disorder 0.400 2 7.59e-8 5.72e-7 ✓ sig.
S-adenosylhomocysteine hydrolase deficiency Sulfur amino acid metabolism disorder 0.400 2 7.59e-8 5.72e-7 ✓ sig.
Amino acid metabolism disorder propionic acidemia 0.074 2 2.74e-6 1.57e-5 ✓ sig.
Amino acid metabolism disorder Hepatic methionine adenosyltransferase deficiency 0.071 2 8.22e-6 4.35e-5 ✓ sig.
Amino acid metabolism disorder S-adenosylhomocysteine hydrolase deficiency 0.071 2 8.22e-6 4.35e-5 ✓ sig.
Glycine n-methyltransferase deficiency S-adenosylhomocysteine hydrolase deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Glycine n-methyltransferase deficiency Sulfur amino acid metabolism disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Glycine n-methyltransferase deficiency Hepatic methionine adenosyltransferase deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Adenosine kinase deficiency Sulfur amino acid metabolism disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hepatic methionine adenosyltransferase deficiency hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Hepatic methionine adenosyltransferase deficiency methionine adenosyltransferase deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase S-adenosylhomocysteine hydrolase deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase Sulfur amino acid metabolism disorder 0.250 1 1.95e-4 5.28e-4 ✓ sig.
methionine adenosyltransferase deficiency S-adenosylhomocysteine hydrolase deficiency 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Amino acid metabolism disorder Cystathioninuria 0.037 1 1.69e-3 2.51e-3 ✓ sig.
Amino acid metabolism disorder hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase 0.037 1 1.69e-3 2.51e-3 ✓ sig.
Amino acid metabolism disorder lysinuric protein intolerance 0.037 1 1.69e-3 2.51e-3 ✓ sig.
Amino acid metabolism disorder methionine adenosyltransferase deficiency 0.037 1 1.69e-3 2.51e-3 ✓ sig.