Disease Clusters | GeDiPNet

Cluster 237

9 diseases · 25 shared-gene connections

9 Diseases

7 Unique genes

0.343 Avg. similarity score

Childhood myocerebrohepatopathy spectrum Most-connected disease (7 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1 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.

Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1 Childhood myocerebrohepatopathy spectrum Mitochondrial recessive ataxia syndrome (includes sando and scae) Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1 Schilder disease Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Childhood myocerebrohepatopathy spectrum	7	7	1
Mitochondrial recessive ataxia syndrome (includes sando and scae)	7	7	1
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	7	7	1
Schilder disease	7	7	1
Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	6	6	5
Mitochondrial hepatopathy	5	5	3
Neonatal convulsions	5	5	3
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1	5	5	1
Fanconi anemia complementation group i	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
POLG	8 / 9	Childhood myocerebrohepatopathy spectrum, Mitochondrial hepatopathy, Mitochondrial recessive ataxia syndrome (includes sando and scae), Neonatal convulsions and 4 more
FANCI	2 / 9	Fanconi anemia complementation group i, Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis
POLGARF	2 / 9	Mitochondrial hepatopathy, Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis
TWNK	2 / 9	Mitochondrial hepatopathy, Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis

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 ⇵
Choline catabolism ALDH7A1	Reactome	1 / 6	286×	3.49e-3	2.83e-2 ✓ sig.
Lysine catabolism ALDH7A1	Reactome	1 / 12	143×	6.97e-3	4.53e-2 ✓ sig.
ERBB2 Regulates Cell Motility DIAPH1	Reactome	1 / 15	114×	8.71e-3	5.22e-2
Histidine metabolism ALDH7A1	KEGG	1 / 22	78.0×	1.28e-2	6.57e-2
Ascorbate and aldarate metabolism ALDH7A1	KEGG	1 / 30	57.2×	1.74e-2	7.88e-2
beta-Alanine metabolism ALDH7A1	KEGG	1 / 31	55.3×	1.79e-2	8.05e-2
One carbon pool by folate ALDH7A1	KEGG	1 / 38	45.2×	2.19e-2	9.03e-2
Glycine, serine and threonine metabolism ALDH7A1	KEGG	1 / 40	42.9×	2.31e-2	9.30e-2
Fanconi Anemia Pathway FANCI	Reactome	1 / 40	42.9×	2.31e-2	9.30e-2
Tryptophan metabolism ALDH7A1	KEGG	1 / 42	40.9×	2.42e-2	9.58e-2
Fatty acid degradation ALDH7A1	KEGG	1 / 43	39.9×	2.48e-2	9.69e-2
Base excision repair POLG	KEGG	1 / 44	39.0×	2.54e-2	9.82e-2
Pyruvate metabolism ALDH7A1	KEGG	1 / 47	36.5×	2.71e-2	1.02e-1
Valine, leucine and isoleucine degradation ALDH7A1	KEGG	1 / 48	35.7×	2.77e-2	1.03e-1
Arginine and proline metabolism ALDH7A1	KEGG	1 / 50	34.3×	2.88e-2	1.06e-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 ⇵
mitochondrial DNA replication POLG, TWNK	GO:0006264	2 / 11	485×	6.60e-6	3.94e-4 ✓ sig.
DNA-templated DNA replication POLG, TWNK	GO:0006261	2 / 41	130×	9.79e-5	3.04e-3 ✓ sig.
glycine betaine biosynthetic process from choline ALDH7A1	GO:0019285	1 / 2	1,335×	7.49e-4	1.23e-2 ✓ sig.
DNA replication POLG, TWNK	GO:0006260	2 / 131	40.8×	1.00e-3	1.46e-2 ✓ sig.
DNA replication proofreading POLG	GO:0045004	1 / 3	890×	1.12e-3	1.55e-2 ✓ sig.
choline catabolic process ALDH7A1	GO:0042426	1 / 4	667×	1.50e-3	1.82e-2 ✓ sig.
sensory perception of sound ALDH7A1, DIAPH1	GO:0007605	2 / 162	33.0×	1.52e-3	1.85e-2 ✓ sig.
protein localization to axon PRICKLE2	GO:0099612	1 / 5	534×	1.87e-3	2.05e-2 ✓ sig.
cellular response to histamine DIAPH1	GO:0071420	1 / 6	445×	2.25e-3	2.24e-2 ✓ sig.
mitochondrial transcription TWNK	GO:0006390	1 / 8	334×	2.99e-3	2.59e-2 ✓ sig.
protein localization to microtubule DIAPH1	GO:0035372	1 / 10	267×	3.74e-3	2.90e-2 ✓ sig.
protein hexamerization TWNK	GO:0034214	1 / 12	222×	4.49e-3	3.17e-2 ✓ sig.
aldehyde metabolic process ALDH7A1	GO:0006081	1 / 13	205×	4.86e-3	3.29e-2 ✓ sig.
regulation of microtubule-based process DIAPH1	GO:0032886	1 / 13	205×	4.86e-3	3.29e-2 ✓ sig.
base-excision repair, gap-filling POLG	GO:0006287	1 / 14	191×	5.23e-3	3.41e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Mitochondrial hepatopathy	Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	0.500	3	1.62e-11	1.61e-10 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Mitochondrial recessive ataxia syndrome (includes sando and scae)	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	Schilder disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1	Schilder disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mitochondrial recessive ataxia syndrome (includes sando and scae)	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mitochondrial recessive ataxia syndrome (includes sando and scae)	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mitochondrial recessive ataxia syndrome (includes sando and scae)	Schilder disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Schilder disease	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Mitochondrial hepatopathy	Mitochondrial recessive ataxia syndrome (includes sando and scae)	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Neonatal convulsions	Schilder disease	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Neonatal convulsions	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Neonatal convulsions	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 1	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Mitochondrial recessive ataxia syndrome (includes sando and scae)	Neonatal convulsions	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Neonatal convulsions	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Mitochondrial hepatopathy	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Mitochondrial hepatopathy	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Mitochondrial hepatopathy	Schilder disease	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Fanconi anemia complementation group i	Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Childhood myocerebrohepatopathy spectrum	Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Schilder disease	Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Mitochondrial recessive ataxia syndrome (includes sando and scae)	Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive, 1	Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis	0.167	1	3.23e-4	6.41e-4 ✓ sig.

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