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Cluster 367

5 diseases · 6 shared-gene connections

5 Diseases

8 Unique genes

0.194 Avg. similarity score

Urea cycle disorder Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: ornithine translocase deficiency 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.

ornithine translocase deficiency Urea cycle disorder Citrullinemia Citrin deficiency Argininosuccinic aciduria

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Urea cycle disorder	4	4	8
Citrullinemia	3	3	3
Citrin deficiency	2	2	1
ornithine translocase deficiency	2	2	1
Argininosuccinic aciduria	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
SLC25A13	3 / 5	Citrin deficiency, Citrullinemia, Urea cycle disorder
SLC25A15	3 / 5	Citrullinemia, ornithine translocase deficiency, Urea cycle disorder
ASL	2 / 5	Argininosuccinic aciduria, Urea cycle disorder
ASS1	2 / 5	Citrullinemia, Urea cycle 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 ⇵
Urea cycle ASS1, ASL, SLC25A15, ARG1, CPS1, NAGS, OTC	Reactome	7 / 10	1,051×	1.34e-22	1.59e-19 ✓ sig.
Arginine biosynthesis ASS1, ASL, ARG1, CPS1, NAGS, OTC	KEGG	6 / 23	392×	6.77e-16	2.59e-13 ✓ sig.
Biosynthesis of amino acids ASS1, ASL, ARG1, CPS1, NAGS, OTC	KEGG	6 / 75	120×	1.34e-12	2.82e-10 ✓ sig.
Alanine, aspartate and glutamate metabolism ASS1, ASL, CPS1	KEGG	3 / 37	122×	1.49e-6	7.42e-5 ✓ sig.
Metabolic pathways ASS1, ASL, ARG1, CPS1, NAGS, OTC	KEGG	6 / 1,563	5.8×	1.07e-4	2.45e-3 ✓ sig.
Aspartate and asparagine metabolism SLC25A13	Reactome	1 / 12	125×	7.97e-3	6.13e-2
Nitrogen metabolism CPS1	KEGG	1 / 17	88.3×	1.13e-2	7.64e-2
Mitochondrial protein import OTC	Reactome	1 / 19	79.0×	1.26e-2	8.17e-2
2-Oxocarboxylic acid metabolism NAGS	KEGG	1 / 33	45.5×	2.18e-2	1.12e-1
Gluconeogenesis SLC25A13	Reactome	1 / 34	44.2×	2.24e-2	1.14e-1
Arginine and proline metabolism ARG1	KEGG	1 / 50	30.0×	3.28e-2	1.41e-1
Amoebiasis ARG1	KEGG	1 / 103	14.6×	6.66e-2	2.05e-1
Carbon metabolism CPS1	KEGG	1 / 115	13.1×	7.41e-2	2.18e-1
Fluid shear stress and atherosclerosis ASS1	KEGG	1 / 141	10.6×	9.02e-2	2.41e-1
Efferocytosis ARG1	KEGG	1 / 157	9.6×	9.99e-2	2.54e-1

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, ASL, SLC25A15, ARG1, CPS1, NAGS, OTC	GO:0000050	7 / 12	1,363×	4.02e-23	1.01e-19 ✓ sig.
L-arginine biosynthetic process ASS1, ASL, NAGS, OTC	GO:0006526	4 / 4	2,336×	1.38e-14	8.87e-12 ✓ sig.
midgut development ASS1, CPS1, OTC	GO:0007494	3 / 8	876×	2.88e-9	5.71e-7 ✓ sig.
amino acid biosynthetic process ASS1, ASL, OTC	GO:0008652	3 / 27	260×	1.50e-7	1.74e-5 ✓ sig.
response to zinc ion ASS1, CPS1, OTC	GO:0010043	3 / 27	260×	1.50e-7	1.74e-5 ✓ sig.
L-arginine biosynthetic process via ornithine ASL, OTC	GO:0042450	2 / 2	2,336×	1.60e-7	1.84e-5 ✓ sig.
monoatomic anion homeostasis CPS1, OTC	GO:0055081	2 / 2	2,336×	1.60e-7	1.84e-5 ✓ sig.
cellular response to oleic acid ASS1, CPS1	GO:0071400	2 / 3	1,557×	4.81e-7	4.64e-5 ✓ sig.
citrulline biosynthetic process CPS1, OTC	GO:0019240	2 / 4	1,168×	9.62e-7	8.18e-5 ✓ sig.
cellular response to ammonium ion ASS1, CPS1	GO:0071242	2 / 5	934×	1.60e-6	1.25e-4 ✓ sig.
arginine metabolic process ASL, ARG1	GO:0006525	2 / 8	584×	4.48e-6	2.83e-4 ✓ sig.
liver development ASS1, CPS1, OTC	GO:0001889	3 / 87	80.5×	5.37e-6	3.29e-4 ✓ sig.
response to amine ASS1, CPS1	GO:0014075	2 / 10	467×	7.20e-6	4.16e-4 ✓ sig.
cellular response to glucagon stimulus ASS1, CPS1	GO:0071377	2 / 11	425×	8.80e-6	4.90e-4 ✓ sig.
response to growth hormone ASS1, CPS1	GO:0060416	2 / 14	334×	1.46e-5	7.25e-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.
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.

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