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Cluster 550

5 diseases · 8 shared-gene connections

5 Diseases

6 Unique genes

0.323 Avg. similarity score

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

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital hypoplasia of aortic arch	4	4	1
Periportal fibrosis	4	4	1
Cystathionine beta-synthase deficiency	3	3	2
Ventricular hypertrophy	3	3	3
Autosomal recessive polycystic kidney disease	2	2	3

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

Gene ⇵	Member diseases ⇵	Linked diseases
PKHD1	5 / 5	Autosomal recessive polycystic kidney disease, Congenital hypoplasia of aortic arch, Cystathionine beta-synthase deficiency, Periportal fibrosis and 1 more

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 ⇵
Cysteine formation from homocysteine CBS	Reactome	1 / 3	667×	1.50e-3	1.54e-2 ✓ sig.
Negative feedback regulation of MAPK pathway BRAF	Reactome	1 / 6	334×	2.99e-3	2.54e-2 ✓ sig.
cAMP signaling pathway BRAF, RYR2	KEGG	2 / 226	17.7×	5.03e-3	3.66e-2 ✓ sig.
Frs2-mediated activation BRAF	Reactome	1 / 12	167×	5.98e-3	4.10e-2 ✓ sig.
Spry regulation of FGF signaling BRAF	Reactome	1 / 16	125×	7.97e-3	4.94e-2 ✓ sig.
VxPx cargo-targeting to cilium PKD1	Reactome	1 / 21	95.3×	1.04e-2	5.84e-2
RAF activation BRAF	Reactome	1 / 32	62.6×	1.59e-2	7.50e-2
Signaling by high-kinase activity BRAF mutants BRAF	Reactome	1 / 36	55.6×	1.79e-2	8.03e-2
Thyroid cancer BRAF	KEGG	1 / 37	54.1×	1.83e-2	8.16e-2
One carbon pool by folate CBS	KEGG	1 / 38	52.7×	1.88e-2	8.28e-2
Negative regulation of MAPK pathway BRAF	Reactome	1 / 38	52.7×	1.88e-2	8.28e-2
Glycine, serine and threonine metabolism CBS	KEGG	1 / 40	50.0×	1.98e-2	8.52e-2
MAP2K and MAPK activation BRAF	Reactome	1 / 40	50.0×	1.98e-2	8.52e-2
Bladder cancer BRAF	KEGG	1 / 41	48.8×	2.03e-2	8.65e-2
Pathways of neurodegeneration - multiple diseases BRAF, RYR2	KEGG	2 / 480	8.3×	2.15e-2	8.93e-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 ⇵
branching morphogenesis of an epithelial tube PKHD1, PKD1	GO:0048754	2 / 29	215×	3.47e-5	1.40e-3 ✓ sig.
regulation of cell adhesion PKHD1, PKD1	GO:0030155	2 / 61	102×	1.56e-4	4.26e-3 ✓ sig.
metanephric distal tubule morphogenesis PKD1	GO:0072287	1 / 1	3,115×	3.21e-4	7.04e-3 ✓ sig.
regulation of cholangiocyte proliferation PKHD1	GO:1904054	1 / 1	3,115×	3.21e-4	7.04e-3 ✓ sig.
establishment of protein localization to endoplasmic reticulum RYR2	GO:0072599	1 / 1	3,115×	3.21e-4	7.04e-3 ✓ sig.
negative regulation of apoptotic process PKHD1, CBS, BRAF	GO:0043066	3 / 524	17.8×	4.12e-4	8.35e-3 ✓ sig.
intracellular calcium ion homeostasis PKHD1, RYR2	GO:0006874	2 / 113	55.1×	5.35e-4	9.88e-3 ✓ sig.
Purkinje myocyte to ventricular cardiac muscle cell signaling RYR2	GO:0086029	1 / 2	1,557×	6.42e-4	1.11e-2 ✓ sig.
nitrogen cycle metabolic process PKD1	GO:0071941	1 / 2	1,557×	6.42e-4	1.11e-2 ✓ sig.
cysteine biosynthetic process from serine CBS	GO:0006535	1 / 2	1,557×	6.42e-4	1.11e-2 ✓ sig.
sulfur compound biosynthetic process CBS	GO:0044272	1 / 2	1,557×	6.42e-4	1.11e-2 ✓ sig.
animal organ morphogenesis BRAF, PKD1	GO:0009887	2 / 130	47.9×	7.07e-4	1.19e-2 ✓ sig.
kidney development PKHD1, PKD1	GO:0001822	2 / 146	42.7×	8.91e-4	1.37e-2 ✓ sig.
calcium ion transmembrane transport RYR2, PKD1	GO:0070588	2 / 149	41.8×	9.28e-4	1.41e-2 ✓ sig.
positive T cell selection BRAF	GO:0043368	1 / 3	1,038×	9.63e-4	1.42e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Congenital hypoplasia of aortic arch	Periportal fibrosis	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Congenital hypoplasia of aortic arch	Cystathionine beta-synthase deficiency	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Congenital hypoplasia of aortic arch	Ventricular hypertrophy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cystathionine beta-synthase deficiency	Periportal fibrosis	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Periportal fibrosis	Ventricular hypertrophy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Autosomal recessive polycystic kidney disease	Congenital hypoplasia of aortic arch	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Autosomal recessive polycystic kidney disease	Periportal fibrosis	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Cystathionine beta-synthase deficiency	Ventricular hypertrophy	0.250	1	2.58e-4	5.38e-4 ✓ sig.

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