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Cluster 387

5 diseases · 4 shared-gene connections

5 Diseases

6 Unique genes

0.143 Avg. similarity score

Congenital bile acid synthesis defect Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

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Congenital bile acid synthesis defect Alpha-methylacyl-coa racemase deficiency congenital bile acid synthesis defect 1 congenital bile acid synthesis defect 2 congenital bile acid synthesis defect 6

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital bile acid synthesis defect	4	4	6
Alpha-methylacyl-coa racemase deficiency	1	1	1
congenital bile acid synthesis defect 1	1	1	1
congenital bile acid synthesis defect 2	1	1	1
congenital bile acid synthesis defect 6	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
ACOX2	2 / 5	Congenital bile acid synthesis defect, congenital bile acid synthesis defect 6
AKR1D1	2 / 5	Congenital bile acid synthesis defect, congenital bile acid synthesis defect 2
AMACR	2 / 5	Alpha-methylacyl-coa racemase deficiency, Congenital bile acid synthesis defect
HSD3B7	2 / 5	Congenital bile acid synthesis defect, congenital bile acid synthesis defect 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 ⇵
Primary bile acid biosynthesis AMACR, HSD3B7, AKR1D1, CYP7B1, ACOX2	KEGG	5 / 17	589×	1.78e-14	5.28e-12 ✓ sig.
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol AMACR, HSD3B7, AKR1D1, CYP7B1, ACOX2	Reactome	5 / 24	417×	1.22e-13	3.07e-11 ✓ sig.
Synthesis of bile acids and bile salts via 24-hydroxycholesterol AMACR, HSD3B7, AKR1D1	Reactome	3 / 14	429×	2.52e-8	1.97e-6 ✓ sig.
Synthesis of bile acids and bile salts via 27-hydroxycholesterol HSD3B7, AKR1D1, CYP7B1	Reactome	3 / 15	400×	3.15e-8	2.39e-6 ✓ sig.
Peroxisome AMACR, ABCD3, ACOX2	KEGG	3 / 83	72.3×	6.27e-6	2.27e-4 ✓ sig.
Beta-oxidation of pristanoyl-CoA AMACR, ACOX2	Reactome	2 / 9	445×	7.48e-6	2.63e-4 ✓ sig.
Steroid hormone biosynthesis AKR1D1, CYP7B1	KEGG	2 / 63	63.5×	4.01e-4	6.72e-3 ✓ sig.
Peroxisomal protein import AMACR, ACOX2	Reactome	2 / 63	63.5×	4.01e-4	6.72e-3 ✓ sig.
Defective CYP7B1 causes Spastic paraplegia 5A, autosomal recessive (SPG5A) and Congenital bile acid synthesis defect 3 (CBAS3) CYP7B1	Reactome	1 / 1	2,002×	5.00e-4	7.96e-3 ✓ sig.
Metabolic pathways AMACR, HSD3B7, AKR1D1, ACOX2	KEGG	4 / 1,563	5.1×	3.45e-3	3.40e-2 ✓ sig.
Synthesis of bile acids and bile salts CYP7B1	Reactome	1 / 14	143×	6.98e-3	5.45e-2
ABC transporters in lipid homeostasis ABCD3	Reactome	1 / 18	111×	8.96e-3	6.42e-2
Class I peroxisomal membrane protein import ABCD3	Reactome	1 / 20	100×	9.95e-3	6.82e-2
Endogenous sterols CYP7B1	Reactome	1 / 25	80.1×	1.24e-2	7.78e-2
ABC transporters ABCD3	KEGG	1 / 45	44.5×	2.23e-2	1.09e-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 ⇵
bile acid biosynthetic process AMACR, HSD3B7, AKR1D1, CYP7B1, ABCD3, ACOX2	GO:0006699	6 / 27	692×	5.01e-18	6.04e-15 ✓ sig.
B cell chemotaxis HSD3B7, CYP7B1	GO:0035754	2 / 6	1,038×	1.29e-6	1.01e-4 ✓ sig.
fatty acid beta-oxidation using acyl-CoA oxidase AMACR, ACOX2	GO:0033540	2 / 14	445×	7.80e-6	4.29e-4 ✓ sig.
very long-chain fatty acid metabolic process ABCD3, ACOX2	GO:0000038	2 / 22	283×	1.98e-5	8.90e-4 ✓ sig.
lipid metabolic process HSD3B7, AKR1D1, CYP7B1, ACOX2	GO:0006629	4 / 840	14.8×	5.66e-5	1.97e-3 ✓ sig.
fatty acid beta-oxidation ABCD3, ACOX2	GO:0006635	2 / 48	130×	9.63e-5	2.94e-3 ✓ sig.
steroid biosynthetic process HSD3B7, CYP7B1	GO:0006694	2 / 65	95.8×	1.77e-4	4.64e-3 ✓ sig.
phytanic acid metabolic process ABCD3	GO:1903512	1 / 2	1,557×	6.42e-4	1.13e-2 ✓ sig.
bile acid catabolic process AKR1D1	GO:0030573	1 / 2	1,557×	6.42e-4	1.13e-2 ✓ sig.
steroid metabolic process AKR1D1, CYP7B1	GO:0008202	2 / 135	46.1×	7.62e-4	1.26e-2 ✓ sig.
long-chain fatty acid import into peroxisome ABCD3	GO:0015910	1 / 4	779×	1.28e-3	1.75e-2 ✓ sig.
fatty acid metabolic process AMACR, ACOX2	GO:0006631	2 / 211	29.5×	1.85e-3	2.17e-2 ✓ sig.
very long-chain fatty acid catabolic process ABCD3	GO:0042760	1 / 6	519×	1.93e-3	2.20e-2 ✓ sig.
C21-steroid hormone metabolic process AKR1D1	GO:0008207	1 / 7	445×	2.25e-3	2.41e-2 ✓ sig.
cholesterol catabolic process AKR1D1	GO:0006707	1 / 9	346×	2.89e-3	2.76e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Alpha-methylacyl-coa racemase deficiency	Congenital bile acid synthesis defect	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Congenital bile acid synthesis defect	congenital bile acid synthesis defect 1	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Congenital bile acid synthesis defect	congenital bile acid synthesis defect 2	0.143	1	3.90e-4	8.52e-4 ✓ sig.
Congenital bile acid synthesis defect	congenital bile acid synthesis defect 6	0.143	1	3.90e-4	8.52e-4 ✓ sig.

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