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Cluster 616

5 diseases · 7 shared-gene connections

5 Diseases

5 Unique genes

0.310 Avg. similarity score

Combined oxidative phosphorylation defect 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.

Combined oxidative phosphorylation defect Deafness, autosomal recessive 70 Deafness, autosomal recessive, 70, with or without adult-onset neurodegeneration Respiratory chain disorder Mitochondrial disease with regression and lactic acidosis

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Combined oxidative phosphorylation defect	4	4	5
Deafness, autosomal recessive 70	3	3	1
Deafness, autosomal recessive, 70, with or without adult-onset neurodegeneration	3	3	1
Respiratory chain disorder	3	3	1
Mitochondrial disease with regression and lactic acidosis	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
PNPT1	4 / 5	Combined oxidative phosphorylation defect, Deafness, autosomal recessive 70, Deafness, autosomal recessive, 70, with or without adult-onset neurodegeneration, Respiratory chain disorder
MTFMT	2 / 5	Combined oxidative phosphorylation defect, Mitochondrial disease with regression and lactic acidosis

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 ⇵
Aminoacyl-tRNA biosynthesis WARS2, MTFMT, NARS2, TARS2	KEGG	4 / 66	146×	4.14e-9	3.37e-7 ✓ sig.
Mitochondrial tRNA aminoacylation WARS2	Reactome	1 / 14	172×	5.82e-3	4.03e-2 ✓ sig.
RNA degradation PNPT1	KEGG	1 / 78	30.8×	3.21e-2	1.12e-1
Metabolic pathways MTFMT	KEGG	1 / 1,563	1.5×	5.02e-1	6.20e-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 ⇵
tRNA aminoacylation for protein translation WARS2, NARS2, TARS2	GO:0006418	3 / 36	311×	6.55e-8	8.91e-6 ✓ sig.
translation WARS2, MTFMT, NARS2, TARS2	GO:0006412	4 / 310	48.2×	3.67e-7	3.75e-5 ✓ sig.
RNA import into mitochondrion PNPT1	GO:0035927	1 / 1	3,737×	2.68e-4	6.25e-3 ✓ sig.
nuclear polyadenylation-dependent mRNA catabolic process PNPT1	GO:0071042	1 / 1	3,737×	2.68e-4	6.25e-3 ✓ sig.
mitochondrial tryptophanyl-tRNA aminoacylation WARS2	GO:0070183	1 / 1	3,737×	2.68e-4	6.25e-3 ✓ sig.
conversion of methionyl-tRNA to N-formyl-methionyl-tRNA MTFMT	GO:0071951	1 / 1	3,737×	2.68e-4	6.25e-3 ✓ sig.
mitochondrial threonyl-tRNA aminoacylation TARS2	GO:0070159	1 / 1	3,737×	2.68e-4	6.25e-3 ✓ sig.
asparaginyl-tRNA aminoacylation NARS2	GO:0006421	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
mitochondrial RNA 5'-end processing PNPT1	GO:0000964	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
tryptophanyl-tRNA aminoacylation WARS2	GO:0006436	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
rRNA import into mitochondrion PNPT1	GO:0035928	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
mitochondrial mRNA catabolic process PNPT1	GO:0000958	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
positive regulation of mitochondrial RNA catabolic process PNPT1	GO:0000962	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
mitochondrial RNA 3'-end processing PNPT1	GO:0000965	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.
threonyl-tRNA aminoacylation TARS2	GO:0006435	1 / 3	1,246×	8.03e-4	1.28e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Deafness, autosomal recessive 70	Respiratory chain disorder	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Deafness, autosomal recessive 70	Deafness, autosomal recessive, 70, with or without adult-onset neurodegeneration	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Deafness, autosomal recessive, 70, with or without adult-onset neurodegeneration	Respiratory chain disorder	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Combined oxidative phosphorylation defect	Respiratory chain disorder	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Combined oxidative phosphorylation defect	Deafness, autosomal recessive 70	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Combined oxidative phosphorylation defect	Deafness, autosomal recessive, 70, with or without adult-onset neurodegeneration	0.167	1	3.23e-4	6.41e-4 ✓ sig.
Combined oxidative phosphorylation defect	Mitochondrial disease with regression and lactic acidosis	0.167	1	3.23e-4	6.41e-4 ✓ sig.

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