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Cluster 421

5 diseases · 8 shared-gene connections

5 Diseases

5 Unique genes

0.275 Avg. similarity score

Congenital vertebral-cardiac-renal anomalies syndrome 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.

Congenital vertebral-cardiac-renal anomalies syndrome Vertebral, cardiac, renal, and limb defects syndrome Catel-manzke syndrome vertebral, cardiac, renal, and limb defects syndrome 2 vertebral, cardiac, renal, and limb defects syndrome 1

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital vertebral-cardiac-renal anomalies syndrome	4	4	3
Vertebral, cardiac, renal, and limb defects syndrome	4	4	4
Catel-manzke syndrome	3	3	2
vertebral, cardiac, renal, and limb defects syndrome 2	3	3	1
vertebral, cardiac, renal, and limb defects syndrome 1	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
KYNU	4 / 5	Catel-manzke syndrome, Congenital vertebral-cardiac-renal anomalies syndrome, Vertebral, cardiac, renal, and limb defects syndrome, vertebral, cardiac, renal, and limb defects syndrome 2
HAAO	3 / 5	Congenital vertebral-cardiac-renal anomalies syndrome, Vertebral, cardiac, renal, and limb defects syndrome, vertebral, cardiac, renal, and limb defects syndrome 1
NADSYN1	2 / 5	Congenital vertebral-cardiac-renal anomalies syndrome, Vertebral, cardiac, renal, and limb defects syndrome

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 ⇵
Tryptophan catabolism KYNU, HAAO	Reactome	2 / 11	437×	7.62e-6	2.67e-4 ✓ sig.
Biosynthesis of cofactors KYNU, HAAO, NADSYN1	KEGG	3 / 154	46.8×	2.03e-5	6.04e-4 ✓ sig.
Tryptophan metabolism KYNU, HAAO	KEGG	2 / 42	114×	1.19e-4	2.57e-3 ✓ sig.
Metabolic pathways KYNU, TGDS, HAAO, NADSYN1	KEGG	4 / 1,563	6.1×	1.28e-3	1.63e-2 ✓ sig.
Nicotinate metabolism NADSYN1	Reactome	1 / 12	200×	4.99e-3	4.37e-2 ✓ sig.
Biosynthesis of various nucleotide sugars TGDS	KEGG	1 / 15	160×	6.23e-3	5.06e-2
Biosynthesis of nucleotide sugars TGDS	KEGG	1 / 37	64.9×	1.53e-2	8.81e-2
Nicotinate and nicotinamide metabolism NADSYN1	KEGG	1 / 38	63.2×	1.57e-2	8.96e-2
Spliceosome WBP11	KEGG	1 / 162	14.8×	6.57e-2	1.98e-1
mRNA Splicing - Major Pathway WBP11	Reactome	1 / 183	13.1×	7.39e-2	2.11e-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 ⇵
'de novo' NAD+ biosynthetic process from L-tryptophan KYNU, HAAO, NADSYN1	GO:0034354	3 / 9	1,246×	7.72e-10	1.78e-7 ✓ sig.
NAD+ biosynthetic process KYNU, HAAO, NADSYN1	GO:0009435	3 / 13	862×	2.63e-9	5.25e-7 ✓ sig.
anthranilate metabolic process KYNU, HAAO	GO:0043420	2 / 3	2,492×	1.72e-7	1.91e-5 ✓ sig.
quinolinate biosynthetic process KYNU, HAAO	GO:0019805	2 / 4	1,869×	3.44e-7	3.40e-5 ✓ sig.
L-tryptophan catabolic process KYNU, HAAO	GO:0006569	2 / 9	831×	2.06e-6	1.47e-4 ✓ sig.
pyridine nucleotide biosynthetic process KYNU, HAAO	GO:0019363	2 / 11	680×	3.15e-6	2.07e-4 ✓ sig.
purine-containing compound metabolic process KYNU	GO:0072521	1 / 1	3,737×	2.68e-4	6.20e-3 ✓ sig.
response to vitamin B6 KYNU	GO:0034516	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
nucleotide-sugar metabolic process TGDS	GO:0009225	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
quinolinate metabolic process HAAO	GO:0046874	1 / 2	1,869×	5.35e-4	9.98e-3 ✓ sig.
L-kynurenine catabolic process KYNU	GO:0097053	1 / 4	934×	1.07e-3	1.57e-2 ✓ sig.
dicarboxylic acid metabolic process HAAO	GO:0043648	1 / 5	747×	1.34e-3	1.79e-2 ✓ sig.
L-tryptophan catabolic process to kynurenine KYNU	GO:0019441	1 / 5	747×	1.34e-3	1.79e-2 ✓ sig.
nucleoside phosphate metabolic process KYNU	GO:0006753	1 / 6	623×	1.60e-3	1.98e-2 ✓ sig.
NAD+ biosynthetic process via the salvage pathway NADSYN1	GO:0034355	1 / 17	220×	4.54e-3	3.50e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Congenital vertebral-cardiac-renal anomalies syndrome	Vertebral, cardiac, renal, and limb defects syndrome	0.600	3	6.58e-12	7.74e-11 ✓ sig.
Catel-manzke syndrome	vertebral, cardiac, renal, and limb defects syndrome 2	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Congenital vertebral-cardiac-renal anomalies syndrome	vertebral, cardiac, renal, and limb defects syndrome 2	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Congenital vertebral-cardiac-renal anomalies syndrome	vertebral, cardiac, renal, and limb defects syndrome 1	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Vertebral, cardiac, renal, and limb defects syndrome	vertebral, cardiac, renal, and limb defects syndrome 2	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Vertebral, cardiac, renal, and limb defects syndrome	vertebral, cardiac, renal, and limb defects syndrome 1	0.200	1	2.60e-4	6.40e-4 ✓ sig.
Catel-manzke syndrome	Congenital vertebral-cardiac-renal anomalies syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Catel-manzke syndrome	Vertebral, cardiac, renal, and limb defects syndrome	0.167	1	5.19e-4	1.04e-3 ✓ sig.

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