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Cluster 157

9 diseases · 16 shared-gene connections

9 Diseases

17 Unique genes

0.258 Avg. similarity score

Caroli disease Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: autosomal recessive polycystic kidney 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.

autosomal recessive polycystic kidney disease Caroli disease Congenital hypoplasia of aortic arch Cystathionine beta-synthase deficiency Periportal fibrosis Ventricular hypertrophy

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Caroli disease	5	5	4
Congenital hypoplasia of aortic arch	5	5	1
Cystathionine beta-synthase deficiency	5	5	2
Periportal fibrosis	5	5	1
autosomal recessive polycystic kidney disease	5	5	3
Ventricular hypertrophy	3	3	3
Anhydramnios	2	2	11
Biliary-renal-neuro-skeletal syndrome	1	1	1
Homocystinuria	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PKHD1	7 / 9	Anhydramnios, autosomal recessive polycystic kidney disease, Caroli disease, Congenital hypoplasia of aortic arch and 3 more
PKD1	3 / 9	Anhydramnios, autosomal recessive polycystic kidney disease, Caroli disease
CBS	2 / 9	Cystathionine beta-synthase deficiency, Homocystinuria
IFT56	2 / 9	Biliary-renal-neuro-skeletal syndrome, Caroli disease

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 ⇵
Renin-angiotensin system ACE, AGT, AGTR1	KEGG	3 / 23	92.1×	4.10e-6	1.74e-4 ✓ sig.
Renin secretion ACE, AGT, AGTR1	KEGG	3 / 69	30.7×	1.17e-4	2.62e-3 ✓ sig.
Diabetic cardiomyopathy ACE, AGT, AGTR1, RYR2	KEGG	4 / 205	13.8×	1.65e-4	3.45e-3 ✓ sig.
Metabolism of Angiotensinogen to Angiotensins ACE, AGT	Reactome	2 / 17	83.1×	2.53e-4	4.81e-3 ✓ sig.
Hypertrophic cardiomyopathy ACE, AGT, RYR2	KEGG	3 / 99	21.4×	3.40e-4	6.11e-3 ✓ sig.
VxPx cargo-targeting to cilium PKD1, PKD2	Reactome	2 / 21	67.3×	3.90e-4	6.81e-3 ✓ sig.
Vascular smooth muscle contraction AGT, AGTR1, BRAF	KEGG	3 / 134	15.8×	8.24e-4	1.21e-2 ✓ sig.
Adrenergic signaling in cardiomyocytes AGT, AGTR1, RYR2	KEGG	3 / 154	13.8×	1.23e-3	1.65e-2 ✓ sig.
Cushing syndrome AGT, AGTR1, BRAF	KEGG	3 / 155	13.7×	1.26e-3	1.67e-2 ✓ sig.
Cortisol synthesis and secretion AGT, AGTR1	KEGG	2 / 65	21.7×	3.72e-3	3.68e-2 ✓ sig.
Cysteine formation from homocysteine CBS	Reactome	1 / 3	235×	4.24e-3	4.04e-2 ✓ sig.
Trafficking of myristoylated proteins to the cilium NPHP3	Reactome	1 / 5	141×	7.06e-3	5.68e-2
Aldosterone synthesis and secretion AGT, AGTR1	KEGG	2 / 98	14.4×	8.28e-3	6.27e-2
Negative feedback regulation of MAPK pathway BRAF	Reactome	1 / 6	118×	8.46e-3	6.37e-2
AGE-RAGE signaling pathway in diabetic complications AGT, AGTR1	KEGG	2 / 101	14.0×	8.77e-3	6.53e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
kidney development ACE, AGT, AGTR1, GREB1L, NPHP3, PKD1, PKD2, PKHD1	GO:0001822	8 / 146	60.2×	2.62e-13	1.34e-10 ✓ sig.
maintenance of blood vessel diameter homeostasis by renin-angiotensin ACE, AGT, AGTR1	GO:0002034	3 / 5	660×	6.25e-9	1.13e-6 ✓ sig.
regulation of systemic arterial blood pressure by renin-angiotensin ACE, AGT, AGTR1	GO:0003081	3 / 6	550×	1.25e-8	2.07e-6 ✓ sig.
mesonephric duct development GREB1L, PKD1, PKD2	GO:0072177	3 / 6	550×	1.25e-8	2.07e-6 ✓ sig.
blood vessel diameter maintenance ACE, AGT, AGTR1, CBS	GO:0097746	4 / 37	119×	3.04e-8	4.47e-6 ✓ sig.
angiotensin-activated signaling pathway ACE, AGT, AGTR1	GO:0038166	3 / 16	206×	3.48e-7	3.54e-5 ✓ sig.
regulation of renal output by angiotensin ACE, AGT	GO:0002019	2 / 2	1,099×	7.79e-7	6.91e-5 ✓ sig.
regulation of vasoconstriction ACE, AGT, AGTR1	GO:0019229	3 / 23	143×	1.10e-6	9.11e-5 ✓ sig.
cilium assembly NPHP3, PKHD1, TMEM67, WDR19, DZIP1L	GO:0060271	5 / 237	23.2×	1.72e-6	1.32e-4 ✓ sig.
renin-angiotensin regulation of aldosterone production AGT, AGTR1	GO:0002018	2 / 3	733×	2.34e-6	1.69e-4 ✓ sig.
regulation of renal sodium excretion AGT, AGTR1	GO:0035813	2 / 3	733×	2.34e-6	1.69e-4 ✓ sig.
metanephric ascending thin limb development PKD1, PKD2	GO:0072218	2 / 4	550×	4.67e-6	2.92e-4 ✓ sig.
blood vessel remodeling ACE, AGT, CBS	GO:0001974	3 / 42	78.5×	7.02e-6	4.07e-4 ✓ sig.
branching involved in ureteric bud morphogenesis EYA1, GREB1L, PKD2	GO:0001658	3 / 45	73.3×	8.67e-6	4.84e-4 ✓ sig.
determination of liver left/right asymmetry NPHP3, PKD2	GO:0071910	2 / 6	366×	1.17e-5	6.08e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
autosomal recessive polycystic kidney disease	Caroli disease	0.333	2	1.52e-7	1.03e-6 ✓ sig.
Anhydramnios	autosomal recessive polycystic kidney disease	0.154	2	1.39e-6	7.96e-6 ✓ sig.
Anhydramnios	Caroli disease	0.143	2	2.78e-6	1.51e-5 ✓ sig.
Congenital hypoplasia of aortic arch	Periportal fibrosis	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Congenital hypoplasia of aortic arch	Cystathionine beta-synthase deficiency	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Cystathionine beta-synthase deficiency	Periportal fibrosis	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Cystathionine beta-synthase deficiency	Homocystinuria	0.333	1	1.30e-4	3.93e-4 ✓ sig.
autosomal recessive polycystic kidney disease	Congenital hypoplasia of aortic arch	0.250	1	1.95e-4	5.35e-4 ✓ sig.
autosomal recessive polycystic kidney disease	Periportal fibrosis	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Congenital hypoplasia of aortic arch	Ventricular hypertrophy	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Periportal fibrosis	Ventricular hypertrophy	0.250	1	1.95e-4	5.35e-4 ✓ sig.
Biliary-renal-neuro-skeletal syndrome	Caroli disease	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Caroli disease	Congenital hypoplasia of aortic arch	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Caroli disease	Periportal fibrosis	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Cystathionine beta-synthase deficiency	Ventricular hypertrophy	0.200	1	3.90e-4	8.67e-4 ✓ sig.
autosomal recessive polycystic kidney disease	Cystathionine beta-synthase deficiency	0.200	1	3.90e-4	8.67e-4 ✓ sig.

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