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Cluster 295

8 diseases · 10 shared-gene connections

8 Diseases

50 Unique genes

0.080 Avg. similarity score

Mitochondrial myopathy Most-connected disease (5 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome 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.

Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome Mitochondrial myopathy Progressive external ophthalmoplegia Mitochondrial dna depletion syndrome Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 3 Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 4

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Mitochondrial myopathy	5	5	17
Progressive external ophthalmoplegia	4	4	13
Mitochondrial dna depletion syndrome	3	3	32
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 3	3	3	1
Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 4	2	2	1
Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression	1	1	1
Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy	1	1	1
Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
TK2	4 / 8	Mitochondrial dna depletion syndrome, Mitochondrial myopathy, Progressive external ophthalmoplegia, Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 3
POLG2	3 / 8	Mitochondrial dna depletion syndrome, Progressive external ophthalmoplegia, Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 4
RRM2B	3 / 8	Mitochondrial dna depletion syndrome, Mitochondrial myopathy, Progressive external ophthalmoplegia
SLC25A4	3 / 8	Mitochondrial dna depletion syndrome, Mitochondrial myopathy, Progressive external ophthalmoplegia
FDX2	2 / 8	Mitochondrial myopathy, Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy
IL1A	2 / 8	Mitochondrial myopathy, Progressive external ophthalmoplegia
IL1B	2 / 8	Mitochondrial myopathy, Progressive external ophthalmoplegia
MSTO1	2 / 8	Mitochondrial myopathy, Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome
POLG	2 / 8	Mitochondrial dna depletion syndrome, Progressive external ophthalmoplegia
RRM1	2 / 8	Mitochondrial dna depletion syndrome, Progressive external ophthalmoplegia
SLC25A42	2 / 8	Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression, Mitochondrial myopathy
TWNK	2 / 8	Mitochondrial dna depletion syndrome, Progressive external ophthalmoplegia

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 ⇵
Nucleotide metabolism RRM2B, RRM1, TK2, DGUOK, DTYMK, TYMP, GUK1	KEGG	7 / 85	19.8×	5.41e-8	3.26e-6 ✓ sig.
Transcriptional activation of mitochondrial biogenesis POLG2, POLRMT, TWNK, SOD2, TFAM	Reactome	5 / 51	23.5×	2.07e-6	7.79e-5 ✓ sig.
Pyrimidine metabolism RRM2B, RRM1, TK2, DTYMK, TYMP	KEGG	5 / 58	20.7×	3.95e-6	1.35e-4 ✓ sig.
Interconversion of nucleotide di- and triphosphates RRM2B, RRM1, DTYMK, GUK1	Reactome	4 / 29	33.1×	5.85e-6	1.87e-4 ✓ sig.
Prion disease SLC25A4, IL1A, IL1B, SOD1, CYTB, IL6, TNF, VDAC1	KEGG	8 / 275	7.0×	1.59e-5	4.31e-4 ✓ sig.
Graft-versus-host disease IL1A, IL1B, IL6, TNF	KEGG	4 / 45	21.4×	3.49e-5	8.21e-4 ✓ sig.
Interleukin-10 signaling IL1A, IL1B, IL6, TNF	Reactome	4 / 47	20.4×	4.16e-5	9.44e-4 ✓ sig.
Mitochondrial transcription initiation POLRMT, TFAM	Reactome	2 / 3	160×	5.08e-5	1.11e-3 ✓ sig.
Influenza A SLC25A4, IL1A, IL1B, IL6, TNF, VDAC1	KEGG	6 / 173	8.3×	7.70e-5	1.54e-3 ✓ sig.
Inflammatory bowel disease IL1A, IL1B, IL6, TNF	KEGG	4 / 66	14.6×	1.58e-4	2.73e-3 ✓ sig.
Antifolate resistance IL1B, IL6, TNF	KEGG	3 / 30	24.0×	2.55e-4	3.97e-3 ✓ sig.
Pertussis IL1A, IL1B, IL6, TNF	KEGG	4 / 78	12.3×	3.02e-4	4.53e-3 ✓ sig.
Propanoate metabolism SUCLA2, SUCLG1, ABAT	KEGG	3 / 32	22.5×	3.09e-4	4.61e-3 ✓ sig.
Drug metabolism - other enzymes RRM2B, RRM1, TK2, TYMP	KEGG	4 / 81	11.9×	3.49e-4	5.06e-3 ✓ sig.
Interleukin-1 processing IL1A, IL1B	Reactome	2 / 8	60.1×	4.68e-4	6.35e-3 ✓ sig.

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, POLG2, POLRMT, RRM2B, TWNK, RRM1, MGME1, DNA2	GO:0006264	8 / 11	272×	2.39e-19	3.46e-16 ✓ sig.
vascular endothelial growth factor production IL1B, IL6, TNF	GO:0010573	3 / 6	187×	3.58e-7	3.68e-5 ✓ sig.
mitochondrial DNA repair MGME1, LIG3, DNA2	GO:0043504	3 / 7	160×	6.26e-7	5.86e-5 ✓ sig.
mitochondrial transcription POLRMT, TWNK, TFAM	GO:0006390	3 / 8	140×	1.00e-6	8.59e-5 ✓ sig.
mitochondrion organization POLG2, SOD2, OPA1, LIG3, CAMKMT, MSTO1	GO:0007005	6 / 130	17.2×	1.25e-6	1.03e-4 ✓ sig.
DNA biosynthetic process POLG, POLG2, TK2, LIG3	GO:0071897	4 / 32	46.7×	1.54e-6	1.23e-4 ✓ sig.
response to copper ion IL1A, SOD1, CYTB	GO:0046688	3 / 12	93.4×	3.90e-6	2.59e-4 ✓ sig.
pyrimidine nucleobase metabolic process RRM1, TYMP	GO:0006206	2 / 2	374×	7.02e-6	4.13e-4 ✓ sig.
positive regulation of neuroinflammatory response IL1B, IL6, TNF	GO:0150078	3 / 16	70.1×	9.85e-6	5.38e-4 ✓ sig.
response to activity SOD2, SCO2, IL6, TNF	GO:0014823	4 / 52	28.7×	1.12e-5	5.93e-4 ✓ sig.
ectopic germ cell programmed cell death IL1A, IL1B, SOD1	GO:0035234	3 / 18	62.3×	1.43e-5	7.18e-4 ✓ sig.
carbohydrate derivative metabolic process TK2, DGUOK, TYMP	GO:1901135	3 / 18	62.3×	1.43e-5	7.18e-4 ✓ sig.
DNA repair POLG, RRM2B, RRM1, TOP3A, FANCI, MGME1, LIG3, DNA2	GO:0006281	8 / 420	7.1×	1.43e-5	7.18e-4 ✓ sig.
ribonucleoside diphosphate metabolic process RRM2B, RRM1	GO:0009185	2 / 3	249×	2.10e-5	9.61e-4 ✓ sig.
deoxyribonucleotide biosynthetic process RRM2B, RRM1	GO:0009263	2 / 3	249×	2.10e-5	9.61e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Mitochondrial dna depletion syndrome	Progressive external ophthalmoplegia	0.179	7	1.35e-16	1.75e-15 ✓ sig.
Mitochondrial myopathy	Progressive external ophthalmoplegia	0.192	5	1.07e-12	1.15e-11 ✓ sig.
Progressive external ophthalmoplegia	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 4	0.071	1	8.39e-4	1.34e-3 ✓ sig.
Progressive external ophthalmoplegia	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 3	0.071	1	8.39e-4	1.34e-3 ✓ sig.
Metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression	Mitochondrial myopathy	0.056	1	1.10e-3	1.65e-3 ✓ sig.
Mitochondrial myopathy	Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	0.056	1	1.10e-3	1.65e-3 ✓ sig.
Mitochondrial myopathy	Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy	0.056	1	1.10e-3	1.65e-3 ✓ sig.
Mitochondrial myopathy	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 3	0.056	1	1.10e-3	1.65e-3 ✓ sig.
Mitochondrial dna depletion syndrome	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal dominant, 4	0.030	1	2.07e-3	2.79e-3 ✓ sig.
Mitochondrial dna depletion syndrome	Progressive external ophthalmoplegia with mitochondrial dna deletions, autosomal recessive 3	0.030	1	2.07e-3	2.79e-3 ✓ sig.

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