Disease table of PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MTDNA DELETIONS OMIM ID: PS157640

Gene-disease associations table

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Gene	Associated with PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MTDNA DELETIONS in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
C10orf2	ClinVar, OMIM, HUMSAVAR	HGNC link	10q24.31	4	PS157640, 607459, PS603041, PS233400
DNA2	ClinVar, OMIM, HUMSAVAR	HGNC link	10q21.3	2	PS157640, PS210600
POLG	ClinVar, OMIM, HUMSAVAR	HGNC link	15q26.1	4	PS157640, 607459, PS603041, 256000
POLG2	ClinVar, OMIM, HUMSAVAR	HGNC link	17q23.3	1	PS157640
RNASEH1	OMIM, HUMSAVAR	HGNC link	2p25.3	1	PS157640
RRM2B	ClinVar, OMIM	HGNC link	8q22.3	2	PS157640, PS603041
SLC25A4	ClinVar, OMIM, HUMSAVAR	HGNC link	4q35.1	2	PS157640, PS603041

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Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By region

Shared region	Number of genes associated with the disease	Genes associated with the disease
10q2	2	C10orf2, DNA2

By arm

Shared arm	Number of genes associated with the disease	Genes associated with the disease
10q	2	C10orf2, DNA2

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
10	2	C10orf2, DNA2

Transcription Factors (TF) annotation from TRRUST

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regulated gene	associated to this disease	# TFs	TFs	# TFs associated with this disease	TFs associated with this disease
RRM2B	YES	4	POU2F1, NFKB1, CREB1, TP53	0

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
POLG2	POLG	Yes	0
DNA2	RNASEH1	No	3	RPA3, RPA2, RPA1
DNA2	SLC25A4	No	2	NXF1, MOV10
C10orf2	SLC25A4	No	1	ICT1
RRM2B	SLC25A4	No	1	MCM2

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from BIOGRID - genetic

Interactions from STRING

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Gene1	Gene2	Direct Interaction	Interaction mode	Number of shared interactors	Shared genes in interaction
POLG2	POLG	Yes	binding	0
DNA2	RNASEH1	No	-	1	RPA1
DNA2	POLG	No	-	1	POLD1
DNA2	RRM2B	No	-	1	UBC
DNA2	SLC25A4	No	-	1	UBC
C10orf2	POLG2	No	-	1	GABPA
RRM2B	SLC25A4	No	-	1	UBC

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from CORUM

Interactions from CENSUS

Interactions from PDB

Gene1	Gene2	Interaction	Number of common interactors	Common genes in interaction
POLG2	POLG	Yes	2	POLG2, POLG

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from manually curated literature

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Gene1	Gene2	Direct interaction	More information
C10orf2	POLG	yes, complex	In vitro, C10orf2 forms in combination with POLG, a processive replication machinery, which can use double-stranded DNA (dsDNA) as template to synthesize single-stranded DNA (ssDNA) molecules. [UniProt]

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KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

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KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
DNA replication	hsa03030	7.48	2	DNA2, RNASEH1
Metabolic pathways	hsa01100	2.49	3	RRM2B, POLG2, POLG

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
DNA replication (hsa03030)	-	7.48	0.013	DNA2, RNASEH1

REACTOME pathways annotation: shared terms / NET-GE enrichment

Shared terms

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REACTOME term	REACTOME term ID	IC	Number of genes with the same term	Genes
Transcriptional activation of mitochondrial biogenesis	R-HSA-2151201	7.62	2	C10orf2, POLG2
Mitochondrial biogenesis	R-HSA-1592230	7.34	2	C10orf2, POLG2
Organelle biogenesis and maintenance	R-HSA-1852241	4.63	2	C10orf2, POLG2
Metabolism	R-HSA-1430728	2.34	2	RRM2B, SLC25A4

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Transcriptional activation of mitochondrial biogenesis (R-HSA-2151201)	-	7.62	0.009	C10orf2, POLG2
Mitochondrial biogenesis (R-HSA-1592230)	-	7.34	0.013	C10orf2, POLG2

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GO - molecular function annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
5'-3' DNA helicase activity (GO:0043139)	7.66	2	DNA2, C10orf2
DNA-directed DNA polymerase activity (GO:0003887)	6.41	2	POLG2, POLG
DNA polymerase activity (GO:0034061)	5.93	2	POLG2, POLG
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters (GO:0016893)	5.83	2	DNA2, RNASEH1
DNA helicase activity (GO:0003678)	5.73	2	DNA2, C10orf2
nucleotidyltransferase activity (GO:0016779)	4.81	2	POLG2, POLG
endonuclease activity (GO:0004519)	4.78	2	DNA2, RNASEH1
helicase activity (GO:0004386)	4.69	2	DNA2, C10orf2
nuclease activity (GO:0004518)	4.33	3	DNA2, RNASEH1, POLG
hydrolase activity, acting on ester bonds (GO:0016788)	3.1	3	DNA2, RNASEH1, POLG

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
5'-3' DNA helicase activity (GO:0043139)	-	7.66	0.001	DNA2, C10orf2
DNA-directed DNA polymerase activity (GO:0003887)	-	6.41	0.007	POLG2, POLG
DNA polymerase activity (GO:0034061)	-	5.93	0.014	POLG2, POLG
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters (GO:0016893)	-	5.83	0.011	DNA2, RNASEH1
DNA helicase activity (GO:0003678)	-	5.73	0.011	DNA2, C10orf2
protease binding (GO:0002020)	NEW	5.08	0.031	C10orf2, POLG
endonuclease activity (GO:0004519)	-	4.78	0.009	DNA2, RNASEH1, C10orf2
nuclease activity (GO:0004518)	-	4.33	0.001	C10orf2, RNASEH1, DNA2, POLG
hydrolase activity, acting on ester bonds (GO:0016788)	-	3.1	0.03	SLC25A4, C10orf2, RNASEH1, DNA2, POLG

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GO - biological process annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
DNA replication, removal of RNA primer (GO:0043137)	8.34	2	DNA2, RNASEH1
mitochondrial DNA replication (GO:0006264)	7.53	3	DNA2, RRM2B, POLG
mitochondrial DNA metabolic process (GO:0032042)	7.09	4	DNA2, POLG2, RRM2B, POLG
DNA-dependent DNA replication (GO:0006261)	6.29	4	DNA2, POLG2, RRM2B, POLG
DNA duplex unwinding (GO:0032508)	5.37	2	DNA2, C10orf2
DNA geometric change (GO:0032392)	5.31	2	DNA2, C10orf2
DNA conformation change (GO:0071103)	4.9	2	DNA2, C10orf2
DNA biosynthetic process (GO:0071897)	4.89	3	DNA2, POLG2, POLG
regulation of signal transduction by p53 class mediator (GO:1901796)	4.63	2	DNA2, RRM2B
DNA replication (GO:0006260)	4.51	5	DNA2, C10orf2, POLG2, RRM2B, POLG

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
mitochondrial DNA replication (GO:0006264)	-	7.53	0.0	DNA2, RRM2B, RNASEH1, C10orf2, POLG
mitochondrial DNA metabolic process (GO:0032042)	-	7.09	0.0	DNA2, RRM2B, RNASEH1, C10orf2, POLG
DNA-dependent DNA replication (GO:0006261)	-	6.29	0.0	POLG2, POLG, C10orf2, RNASEH1, DNA2, RRM2B
DNA replication (GO:0006260)	-	4.51	0.0	POLG2, POLG, C10orf2, RNASEH1, RRM2B, DNA2
nucleic acid phosphodiester bond hydrolysis (GO:0090305)	-	4.12	0.013	DNA2, RNASEH1, C10orf2, POLG
DNA repair (GO:0006281)	-	3.59	0.047	DNA2, POLG2, RRM2B, POLG
cellular response to DNA damage stimulus (GO:0006974)	-	3.17	0.025	POLG2, RRM2B, RNASEH1, DNA2, POLG
DNA metabolic process (GO:0006259)	-	3.09	0.002	POLG2, POLG, C10orf2, RNASEH1, DNA2, RRM2B
cellular macromolecule biosynthetic process (GO:0034645)	-	1.66	0.03	POLG2, POLG, C10orf2, RNASEH1, RRM2B, DNA2
macromolecule biosynthetic process (GO:0009059)	-	1.61	0.042	POLG2, POLG, C10orf2, RNASEH1, RRM2B, DNA2

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GO - cellular component annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
gamma DNA polymerase complex (GO:0005760)	9.11	2	DNA2, POLG
DNA polymerase complex (GO:0042575)	7.16	2	DNA2, POLG
mitochondrial nucleoid (GO:0042645)	6.02	3	DNA2, POLG2, POLG
nucleoid (GO:0009295)	5.97	3	DNA2, POLG2, POLG
mitochondrial protein complex (GO:0098798)	4.78	2	DNA2, POLG
transferase complex, transferring phosphorus-containing groups (GO:0061695)	4.61	2	DNA2, POLG
transferase complex (GO:1990234)	3.32	2	DNA2, POLG
mitochondrial part (GO:0044429)	2.92	4	SLC25A4, DNA2, POLG2, POLG
catalytic complex (GO:1902494)	2.9	3	DNA2, RRM2B, POLG
mitochondrion (GO:0005739)	2.42	5	SLC25A4, DNA2, POLG2, RRM2B, POLG

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
mitochondrial nucleoid (GO:0042645)	-	6.02	0.0	C10orf2, POLG2, DNA2, POLG
nucleoid (GO:0009295)	-	5.97	0.0	DNA2, POLG2, C10orf2, POLG
chromosome (GO:0005694)	NEW	3.78	0.016	DNA2, POLG2, POLG
mitochondrial part (GO:0044429)	-	2.92	0.0	SLC25A4, DNA2, POLG2, C10orf2, POLG
mitochondrion (GO:0005739)	-	2.42	0.025	SLC25A4, POLG2, RNASEH1, POLG

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