Disease Clusters | GeDiPNet

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Cluster 365

5 diseases · 7 shared-gene connections

5 Diseases

7 Unique genes

0.273 Avg. similarity score

Dihydropyrimidine metabolism disorder Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Dihydropyrimidine metabolism disorder 1p21.3 microdeletion syndrome Anal polyp Dihydropyrimidine dehydrogenase deficiency Dihydropyrimidinase deficiency

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Dihydropyrimidine metabolism disorder	4	4	2
1p21.3 microdeletion syndrome	3	3	1
Anal polyp	3	3	6
Dihydropyrimidine dehydrogenase deficiency	3	3	1
Dihydropyrimidinase deficiency	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
DPYD	4 / 5	1p21.3 microdeletion syndrome, Anal polyp, Dihydropyrimidine dehydrogenase deficiency, Dihydropyrimidine metabolism disorder
DPYS	2 / 5	Dihydropyrimidinase deficiency, Dihydropyrimidine 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 ⇵
Pyrimidine catabolism DPYD, DPYS	Reactome	2 / 11	312×	1.60e-5	4.96e-4 ✓ sig.
Pantothenate and CoA biosynthesis DPYD, DPYS	KEGG	2 / 21	163×	6.08e-5	1.50e-3 ✓ sig.
beta-Alanine metabolism DPYD, DPYS	KEGG	2 / 31	111×	1.34e-4	2.85e-3 ✓ sig.
Pyrimidine metabolism DPYD, DPYS	KEGG	2 / 58	59.2×	4.74e-4	7.65e-3 ✓ sig.
Drug metabolism - other enzymes DPYD, DPYS	KEGG	2 / 81	42.4×	9.23e-4	1.28e-2 ✓ sig.
Synthesis of Prostaglandins (PG) and Thromboxanes (TX) PTGES	Reactome	1 / 12	143×	6.97e-3	5.45e-2
Arachidonic acid metabolism PTGES	KEGG	1 / 63	27.2×	3.62e-2	1.44e-1
Metabolic pathways DPYD, PTGES, DPYS	KEGG	3 / 1,563	3.3×	5.13e-2	1.74e-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 ⇵
uracil catabolic process DPYD, DPYS	GO:0006212	2 / 2	2,670×	1.20e-7	1.41e-5 ✓ sig.
thymine catabolic process DPYD, DPYS	GO:0006210	2 / 3	1,780×	3.61e-7	3.55e-5 ✓ sig.
CMP catabolic process DPYD, DPYS	GO:0006248	2 / 5	1,068×	1.20e-6	9.61e-5 ✓ sig.
dCMP catabolic process DPYD, DPYS	GO:0006249	2 / 6	890×	1.80e-6	1.33e-4 ✓ sig.
UMP catabolic process DPYD, DPYS	GO:0046050	2 / 6	890×	1.80e-6	1.33e-4 ✓ sig.
dUMP catabolic process DPYD, DPYS	GO:0046079	2 / 6	890×	1.80e-6	1.33e-4 ✓ sig.
pyrimidine nucleobase catabolic process DPYD, DPYS	GO:0006208	2 / 7	763×	2.52e-6	1.73e-4 ✓ sig.
purine nucleobase catabolic process DPYD	GO:0006145	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
thymidine catabolic process DPYD	GO:0006214	1 / 1	2,670×	3.75e-4	7.81e-3 ✓ sig.
beta-alanine biosynthetic process DPYD	GO:0019483	1 / 2	1,335×	7.49e-4	1.25e-2 ✓ sig.
regulation of fever generation PTGES	GO:0031620	1 / 2	1,335×	7.49e-4	1.25e-2 ✓ sig.
negative regulation of RNA splicing PTBP2	GO:0033119	1 / 6	445×	2.25e-3	2.41e-2 ✓ sig.
positive regulation of protein tyrosine kinase activity GPRC5B	GO:0061098	1 / 9	297×	3.37e-3	3.01e-2 ✓ sig.
positive regulation of prostaglandin secretion PTGES	GO:0032308	1 / 9	297×	3.37e-3	3.01e-2 ✓ sig.
regulation of neural precursor cell proliferation PTBP2	GO:2000177	1 / 11	243×	4.11e-3	3.32e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
1p21.3 microdeletion syndrome	Dihydropyrimidine dehydrogenase deficiency	0.500	1	6.49e-5	2.34e-4 ✓ sig.
1p21.3 microdeletion syndrome	Dihydropyrimidine metabolism disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Dihydropyrimidinase deficiency	Dihydropyrimidine metabolism disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Dihydropyrimidine dehydrogenase deficiency	Dihydropyrimidine metabolism disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
1p21.3 microdeletion syndrome	Anal polyp	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Anal polyp	Dihydropyrimidine dehydrogenase deficiency	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Anal polyp	Dihydropyrimidine metabolism disorder	0.125	1	7.79e-4	1.39e-3 ✓ sig.

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