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Cluster 156

9 diseases · 19 shared-gene connections

9 Diseases

22 Unique genes

0.285 Avg. similarity score

Colpocephaly Most-connected disease (6 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Retinal arterial tortuosity 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.

Retinal arterial tortuosity Colpocephaly Familial hematuria-retinal arteriolar tortuosity-contractures syndrome COL4A1-related disorder Prion disease Cerebral microangiopathy

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Colpocephaly	6	6	1
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	6	6	1
Retinal arterial tortuosity	6	6	1
COL4A1-related disorder	5	5	1
Prion disease	5	5	17
Cerebral microangiopathy	4	4	4
Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps	4	4	2
Dementia in huntington’s disease	1	1	2
Intellectual developmental disorder hypotonia spastic sleep	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
COL4A1	7 / 9	Cerebral microangiopathy, COL4A1-related disorder, Colpocephaly, Familial hematuria-retinal arteriolar tortuosity-contractures syndrome and 3 more
ANK3	2 / 9	Intellectual developmental disorder hypotonia spastic sleep, Prion disease
PRNP	2 / 9	Dementia in huntington’s disease, Prion 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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
Collagen biosynthesis and modifying enzymes COL4A1, ADAMTS14	Reactome	2 / 67	16.3×	6.59e-3	5.28e-2
Threonine catabolism RIDA	Reactome	1 / 4	136×	7.31e-3	5.64e-2
Glycerophospholipid biosynthesis AGK	Reactome	1 / 5	109×	9.13e-3	6.54e-2
SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion SEMA3A	Reactome	1 / 10	54.6×	1.82e-2	9.97e-2
Interaction between L1 and Ankyrins ANK3	Reactome	1 / 13	42.0×	2.36e-2	1.15e-1
Sema3A PAK dependent Axon repulsion SEMA3A	Reactome	1 / 15	36.4×	2.71e-2	1.25e-1
Extracellular matrix organization COL4A1	Reactome	1 / 15	36.4×	2.71e-2	1.25e-1
Anchoring fibril formation COL4A1	Reactome	1 / 15	36.4×	2.71e-2	1.25e-1
CRMPs in Sema3A signaling SEMA3A	Reactome	1 / 16	34.1×	2.89e-2	1.29e-1
Insertion of tail-anchored proteins into the endoplasmic reticulum membrane PRNP	Reactome	1 / 16	34.1×	2.89e-2	1.29e-1
Crosslinking of collagen fibrils COL4A1	Reactome	1 / 18	30.3×	3.25e-2	1.38e-1
Translesion Synthesis by POLH RCHY1	Reactome	1 / 19	28.7×	3.43e-2	1.42e-1
NCAM1 interactions COL4A1	Reactome	1 / 21	26.0×	3.78e-2	1.50e-1
Non-integrin membrane-ECM interactions COL4A1	Reactome	1 / 24	22.7×	4.31e-2	1.62e-1
Laminin interactions COL4A1	Reactome	1 / 28	19.5×	5.01e-2	1.76e-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 ⇵
response to copper ion PRNP, SOD1	GO:0046688	2 / 12	142×	8.67e-5	2.72e-3 ✓ sig.
positive regulation of protein targeting to membrane PRNP, ANK3	GO:0090314	2 / 27	62.9×	4.56e-4	9.07e-3 ✓ sig.
neuronal action potential ANK3, SOD1	GO:0019228	2 / 34	50.0×	7.25e-4	1.24e-2 ✓ sig.
neuromuscular junction development COL4A1, ANK3	GO:0007528	2 / 35	48.5×	7.69e-4	1.29e-2 ✓ sig.
positive regulation of cell communication by electrical coupling ANK3	GO:0010650	1 / 1	849×	1.18e-3	1.67e-2 ✓ sig.
L-threonine catabolic process to glycine RIDA	GO:0019518	1 / 1	849×	1.18e-3	1.67e-2 ✓ sig.
placenta development HTRA1, SOD1	GO:0001890	2 / 48	35.4×	1.44e-3	1.90e-2 ✓ sig.
maintenance of protein location in plasma membrane ANK3	GO:0072660	1 / 2	425×	2.35e-3	2.52e-2 ✓ sig.
positive regulation of membrane depolarization during cardiac muscle cell action potential ANK3	GO:1900827	1 / 2	425×	2.35e-3	2.52e-2 ✓ sig.
response to antipsychotic drug SOD1	GO:0097332	1 / 2	425×	2.35e-3	2.52e-2 ✓ sig.
cellular response to amino acid stimulus COL4A1, CPEB4	GO:0071230	2 / 64	26.5×	2.55e-3	2.64e-2 ✓ sig.
basal dendrite arborization SEMA3A	GO:0150020	1 / 3	283×	3.53e-3	3.12e-2 ✓ sig.
positive regulation of heparan sulfate proteoglycan biosynthetic process PXYLP1	GO:0010909	1 / 3	283×	3.53e-3	3.12e-2 ✓ sig.
regulation of glutamate receptor signaling pathway PRNP	GO:1900449	1 / 3	283×	3.53e-3	3.12e-2 ✓ sig.
regulation of calcium ion import across plasma membrane PRNP	GO:1905664	1 / 3	283×	3.53e-3	3.12e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	Retinal arterial tortuosity	0.500	1	6.49e-5	2.33e-4 ✓ sig.
COL4A1-related disorder	Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
COL4A1-related disorder	Colpocephaly	0.500	1	6.49e-5	2.33e-4 ✓ sig.
COL4A1-related disorder	Retinal arterial tortuosity	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Colpocephaly	Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Colpocephaly	Retinal arterial tortuosity	0.500	1	6.49e-5	2.33e-4 ✓ sig.
Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps	Retinal arterial tortuosity	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps	0.333	1	1.30e-4	3.93e-4 ✓ sig.
COL4A1-related disorder	Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Colpocephaly	Hereditary angiopathy with nephropathy, aneurysms, and muscle cramps	0.333	1	1.30e-4	3.93e-4 ✓ sig.
Cerebral microangiopathy	Colpocephaly	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Cerebral microangiopathy	COL4A1-related disorder	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Cerebral microangiopathy	Retinal arterial tortuosity	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Cerebral microangiopathy	Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	0.200	1	2.60e-4	6.51e-4 ✓ sig.
Intellectual developmental disorder hypotonia spastic sleep	Prion disease	0.056	1	1.10e-3	1.83e-3 ✓ sig.
Familial hematuria-retinal arteriolar tortuosity-contractures syndrome	Prion disease	0.056	1	1.10e-3	1.83e-3 ✓ sig.
Colpocephaly	Prion disease	0.056	1	1.10e-3	1.83e-3 ✓ sig.
Prion disease	Retinal arterial tortuosity	0.056	1	1.10e-3	1.83e-3 ✓ sig.
Dementia in huntington’s disease	Prion disease	0.053	1	2.21e-3	3.11e-3 ✓ sig.

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