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	1. Gene summary of enriched editing regions
	2. Tumor-specific enriched editing regions
	Comparison of enriched editing regions between tumor and normal.
	Correlation of enriched editing regions with tumor stages.
	Associations of enriched editing regions with cancer survival.
	3. Enriched editing regions and immune related genes
	4. Enriched editing regions and immune related splicing
	5. Enriched editing regions and immune infiltration
	6. Enriched editing regions and immune gene sets
	Correlation of enriched editing regions with epithelial-mesenchymal transition.
	Correlations of enriched editing regions with hypoxic.
	Associations of enriched editing regions with hallmark gene sets from MSigDB.
	7. Enriched editing regions and drugs
	Correlations between enriched editing regions and drug sensitivity.
	Enriched editing regions targeted by drugs from DrugBank database.

Editing gene: ERVK3-1 (ImmuneEditome ID:105372481)

1. Gene summary of enriched editing regions for ERVK3-1

Gene summary

Gene information	Gene symbol	ERVK3-1
	Gene ID	105372481
	GeneSynonyms	-
	GeneCytomap	19q13.43
	GeneType	protein-coding
	GeneDescription	endogenous retrovirus group K3 member 1\|HERV-K(HML6-1)
	GeneModificationdate	20230329
	UniprotID	Q96A10;B3KNS4;A0A0U1RQN3;A0A0U1RQV1;A0A0U1RQS5;A0A0U1RQL9
	PubMed ID

UCSC image.

Locations of each EERs.

EER	ENST	ENSG	GeneName	Region	Repeat	dsRNA structure
chr19:58313312-58314617:+	ENST00000413518.4	ENSG00000142396.9	ERVK3-1	ncRNA_intronic	AluY,AluSg7,HERVK3-int	chr19:58313312-58314617:+.alignment
chr19:58313312-58314617:+	ENST00000427361.4	ENSG00000142396.9	ERVK3-1	ncRNA_intronic	AluY,AluSg7,HERVK3-int	chr19:58313312-58314617:+.alignment
chr19:58313312-58314617:+	ENST00000590505.1	ENSG00000142396.9	ERVK3-1	ncRNA_intronic	AluY,AluSg7,HERVK3-int	chr19:58313312-58314617:+.alignment
chr19:58313312-58314617:+	ENST00000610038.4	ENSG00000142396.9	ERVK3-1	ncRNA_intronic	AluY,AluSg7,HERVK3-int	chr19:58313312-58314617:+.alignment

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2. Tumor-specific enriched editing regions for ERVK3-1

Comparison of enriched editing regions between tumor and normal.

* P<0.05 and Informative number >=20.

* EER: enriched editing region, EAG: EER-associated genes.

ID_events

cancer

Type

Boxplot

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Correlation of enriched editing regions with tumor stages.

* AnovaP<0.05, Pearson P<0.05 and Informative number >=20.

* EER: enriched editing region, EAG: EER-associated genes, Path: Pathological stage, Cli: Clinical stage.

* Only shows the most significant correlation result of EERs/EAGs with either pathological stage or clinical stage according to correlation coefficient (R). For more results, please go to download page.

ID_events

cancer

Type

StageType

AnovaP

Boxplot

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Associations of enriched editing regions with cancer survival.

* Pkm<0.05 and Pcox<0.05.

* EER: enriched editing region, EAG: EER-associated genes.

ID_events	cancer	TypeID	Pkm	Pcox_continuous	HR_continuous	KMPlot
chr19:58313312-58314617:+	UCEC	EER	2.0206e-03	3.8705e-02	1.1353e+04
ENSG00000142396.9,ERVK3-1	UCEC	EAG	2.0206e-03	3.8705e-02	1.1353e+04

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3. Enriched editing regions and immune related genes for ERVK3-1

Enriched editing regions and immune related genes.

* First, the associations between enriched editing regions and genes were tested by QTL and Pearson method (QTL: FDR<0.05 and Pearson: P<0.05).

* Second, the gene relationships with immune were tested by three analyses: whether the gene is an immune gene (InnateDB、Immport、Immunome、Immunogenetic Related Information Source (IRIS)), whether the gene is associated with immune infiltration and whether the gene is related to immune gene sets.

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the most significant correlation result of genes with the fraction of different immune cells and the scores of 50 hallmark genesets according to correlation coefficient (R). For more results, please go to download page.

ID_events

cancer

Type

Gene

beta

FDR

PearsonP

PearsonR

CorrelationPlot

RBP

RBPtargets

ImmuneGene

ImmuneFraction

HallMark

More results

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4. Enriched editing regions and immune related splicing for ERVK3-1

Enriched editing regions and immune related splicing.

* First, the associations between enriched editing regions and splicing events were tested by QTL and Pearson method (QTL: FDR<0.05 and Pearson: P<0.05).

* Second, the splicing relationships with immune were tested by three analyses: whether the splicing event locates in an immune gene (InnateDB、Immport, Immunome and Immunogenetic Related Information Source (IRIS)), whether the splicing event is associated with immune infiltration and whether the splicing event is related to immune gene sets.

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the most significant correlation result of splicing events with the fraction of different immune cells and the scores of 50 hallmark genesets according to correlation coefficient (R). For more results, please go to download page.

ID_events

cancer

Type

SplicingType

SplicingGene

SplicingChr

SplicingPosition

beta

FDR

PearsonP

PearsonR

CorrelationPlot

RBP

RBPtargets

ImmuneGene

ImmuneFraction

HallMark

More results

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5. Enriched editing regions and immune infiltration for ERVK3-1

Associations of enriched editing regions with immune infiltration.

* P<0.05 and Informative number >=20.

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the most significant correlation result of EERs/EAGs with the fraction of different immune cells according to correlation coefficient (R). For more results, please go to download page.

ID_events	cancer	TypeID	ImmuneCell	P	R	CorrelationPlot
chr19:58313312-58314617:+	BRCA	EER	T_cells_CD4_memory_resting	2.6821e-02	-0.1418
ENSG00000142396.9,ERVK3-1	BRCA	EAG	T_cells_CD4_memory_resting	2.6821e-02	-0.1418
chr19:58313312-58314617:+	CESC	EER	T_cells_CD8	3.8317e-02	0.2801
ENSG00000142396.9,ERVK3-1	CESC	EAG	T_cells_CD8	3.8317e-02	0.2801
chr19:58313312-58314617:+	ESCA	EER	NK_cells_activated	1.6583e-02	0.2548
ENSG00000142396.9,ERVK3-1	ESCA	EAG	NK_cells_activated	1.6583e-02	0.2548
chr19:58313312-58314617:+	GBM	EER	Macrophages_M0	7.2808e-03	-0.3991
ENSG00000142396.9,ERVK3-1	GBM	EAG	Macrophages_M0	7.2808e-03	-0.3991
ENSG00000142396.9,ERVK3-1	HNSC	EAG	Dendritic_cells_activated	3.3920e-02	0.4644
chr19:58313312-58314617:+	KIRC	EER	T_cells_CD4_memory_activated	3.1970e-02	-0.3315
ENSG00000142396.9,ERVK3-1	KIRC	EAG	T_cells_CD4_memory_activated	3.1970e-02	-0.3315
ENSG00000142396.9,ERVK3-1	LUAD	EAG	T_cells_CD4_memory_activated	2.6029e-02	0.2428
chr19:58313312-58314617:+	OV	EER	T_cells_regulatory_(Tregs)	3.2794e-02	-0.1738
ENSG00000142396.9,ERVK3-1	OV	EAG	T_cells_regulatory_(Tregs)	3.2794e-02	-0.1738
chr19:58313312-58314617:+	PCPG	EER	Mast_cells_resting	2.9850e-02	-0.4109
ENSG00000142396.9,ERVK3-1	PCPG	EAG	Mast_cells_resting	2.9850e-02	-0.4109
chr19:58313312-58314617:+	PRAD	EER	T_cells_gamma_delta	3.8266e-02	0.2252
ENSG00000142396.9,ERVK3-1	PRAD	EAG	T_cells_gamma_delta	3.8266e-02	0.2252
ENSG00000142396.9,ERVK3-1	SKCM	EAG	B_cells_memory	4.2930e-03	0.3760
chr19:58313312-58314617:+	STAD	EER	Macrophages_M0	3.1644e-02	0.1576
ENSG00000142396.9,ERVK3-1	STAD	EAG	Macrophages_M0	2.8712e-02	0.1604
ENSG00000142396.9,ERVK3-1	THCA	EAG	Macrophages_M2	2.3673e-02	0.2320

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6. Enriched editing regions and immune gene sets for ERVK3-1

Correlation of enriched editing regions with epithelial-mesenchymal transition.

* First, the differences of enriched editing regions between Epi and Mes groups (defined by KS-test) were compared (P<0.05 and Informative number >=20).

* Second, the correlations between enriched editing regions and gene set score of HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION were analyzed (P<0.05 and Informative number >=20).

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the EERs/EAGs significantly edited between Epi and Mes group.

ID_events

cancer

Type

E2M_P

Boxplot

CorP

CorR

CorrelationPlot

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Correlations of enriched editing regions with hypoxic.

* First, there are four hypoxia scores used in the database. The first three hypoxic scores were calculated on three gene sets of Buffa, Ragnum and Winter based on one previous study (PMID: 32024819). One last hypoxia score was defined on HALLMARK_HYPOXIA by GSVA method.

* Second, the correlations enriched editing regions with the four hypoxic scores were analyzed (P<0.05 and Informative number >=20).

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the EERs/EAGs significantly correlated with all four hypoxia gene set scores. For more results, please go to download page.

ID_events

cancer

Type

Buffa_P

Buffa_R

Ragnum_P

Ragnum_R

Winter_P

Winter_R

HALLMARK_P

HALLMARK_R

CorrelationPlot

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Associations of enriched editing regions with hallmark gene sets from MSigDB.

* P<0.05 and Informative number >=20.

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the most significant correlation result of EERs/EAGs with the scores of 50 hallmark genesets according to correlation coefficient (R). For more results, please go to download page.

ID_events	cancer	HallmarkType	Type	P	R	CorrelationPlot
ENSG00000142396.9,ERVK3-1	BLCA	GSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION	EAG	2.5479e-02	0.2102
chr19:58313312-58314617:+	BLCA	GSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION	EER	2.5479e-02	0.2102
ENSG00000142396.9,ERVK3-1	BRCA	GSVA_HALLMARK_DNA_REPAIR	EAG	4.1679e-03	0.1828
chr19:58313312-58314617:+	BRCA	GSVA_HALLMARK_DNA_REPAIR	EER	4.1679e-03	0.1828
ENSG00000142396.9,ERVK3-1	CESC	GSVA_HALLMARK_MITOTIC_SPINDLE	EAG	9.2036e-04	-0.4344
chr19:58313312-58314617:+	CESC	GSVA_HALLMARK_MITOTIC_SPINDLE	EER	9.2036e-04	-0.4344
ENSG00000142396.9,ERVK3-1	ESCA	GSVA_HALLMARK_HYPOXIA	EAG	1.2093e-03	0.3396
chr19:58313312-58314617:+	ESCA	GSVA_HALLMARK_HYPOXIA	EER	1.2093e-03	0.3396
ENSG00000142396.9,ERVK3-1	HNSC	GSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY	EAG	1.8153e-02	0.5101
chr19:58313312-58314617:+	KIRC	GSVA_HALLMARK_XENOBIOTIC_METABOLISM	EER	4.2073e-03	0.4327
ENSG00000142396.9,ERVK3-1	KIRC	GSVA_HALLMARK_XENOBIOTIC_METABOLISM	EAG	4.2073e-03	0.4327
ENSG00000142396.9,ERVK3-1	LGG	GSVA_HALLMARK_ADIPOGENESIS	EAG	2.4377e-02	0.2880
ENSG00000142396.9,ERVK3-1	LUAD	GSVA_HALLMARK_COMPLEMENT	EAG	2.4616e-02	0.2451
ENSG00000142396.9,ERVK3-1	OV	GSVA_HALLMARK_KRAS_SIGNALING_DN	EAG	1.3623e-02	0.2004
chr19:58313312-58314617:+	OV	GSVA_HALLMARK_KRAS_SIGNALING_DN	EER	1.3623e-02	0.2004
chr19:58313312-58314617:+	PAAD	GSVA_HALLMARK_GLYCOLYSIS	EER	3.2302e-02	0.3917
ENSG00000142396.9,ERVK3-1	PAAD	GSVA_HALLMARK_GLYCOLYSIS	EAG	3.2302e-02	0.3917
chr19:58313312-58314617:+	PRAD	GSVA_HALLMARK_BILE_ACID_METABOLISM	EER	4.1193e-02	0.2220
ENSG00000142396.9,ERVK3-1	PRAD	GSVA_HALLMARK_BILE_ACID_METABOLISM	EAG	4.1193e-02	0.2220
ENSG00000142396.9,ERVK3-1	SKCM	GSVA_HALLMARK_P53_PATHWAY	EAG	1.2720e-02	-0.3310
chr19:58313312-58314617:+	STAD	GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS	EER	1.5040e-02	0.1781
ENSG00000142396.9,ERVK3-1	STAD	GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS	EAG	1.2411e-02	0.1830
ENSG00000142396.9,ERVK3-1	THYM	GSVA_HALLMARK_ANDROGEN_RESPONSE	EAG	3.1867e-02	0.3862
chr19:58313312-58314617:+	UCS	GSVA_HALLMARK_FATTY_ACID_METABOLISM	EER	6.3215e-03	0.5520
ENSG00000142396.9,ERVK3-1	UCS	GSVA_HALLMARK_FATTY_ACID_METABOLISM	EAG	6.3215e-03	0.5520

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7. Enriched editing regions and drugs for ERVK3-1

Correlations between enriched editing regions and drug sensitivity.

* First, the drug sensitivity (IS50) was estimated on 84 drugs by pRRophetic package.

* Second, the correlations between editing enriched regions and drug sensitivity were analyzed (P<0.05 and Informative number >=20).

* EER: enriched editing region, EAG: EER-associated genes.

* Only shows the most significant correlation result of EERs/EAGs with the IS50 scores of 84 drugs according to correlation coefficient (R). For more results, please go to download page.

ID_events	cancer	Drug	Type	P	R	CorrelationPlot
ENSG00000142396.9,ERVK3-1	BLCA	CGP.082996	EAG	1.6076e-02	-0.2260
chr19:58313312-58314617:+	BLCA	CGP.082996	EER	1.6076e-02	-0.2260
ENSG00000142396.9,ERVK3-1	BRCA	AMG.706	EAG	1.3934e-02	-0.1572
chr19:58313312-58314617:+	BRCA	AMG.706	EER	1.3934e-02	-0.1572
ENSG00000142396.9,ERVK3-1	CESC	Imatinib	EAG	2.1333e-03	0.4055
chr19:58313312-58314617:+	CESC	Imatinib	EER	2.1333e-03	0.4055
ENSG00000142396.9,ERVK3-1	ESCA	BI.D1870	EAG	3.0144e-05	-0.4292
chr19:58313312-58314617:+	ESCA	BI.D1870	EER	3.0144e-05	-0.4292
ENSG00000142396.9,ERVK3-1	GBM	AICAR	EAG	2.8748e-03	-0.4390
chr19:58313312-58314617:+	GBM	AICAR	EER	2.8748e-03	-0.4390
ENSG00000142396.9,ERVK3-1	HNSC	CCT018159	EAG	2.1293e-04	-0.7230
chr19:58313312-58314617:+	KIRC	BI.2536	EER	3.0471e-03	0.4464
ENSG00000142396.9,ERVK3-1	KIRC	BI.2536	EAG	3.0471e-03	0.4464
ENSG00000142396.9,ERVK3-1	KIRP	Metformin	EAG	9.9949e-03	-0.4238
chr19:58313312-58314617:+	KIRP	Metformin	EER	9.9949e-03	-0.4238
chr19:58313312-58314617:+	LAML	ABT.888	EER	1.7888e-02	-0.3515
ENSG00000142396.9,ERVK3-1	LAML	ABT.888	EAG	1.7888e-02	-0.3515
ENSG00000142396.9,ERVK3-1	LGG	FH535	EAG	2.1634e-02	-0.2936
ENSG00000142396.9,ERVK3-1	LUAD	Gemcitabine	EAG	2.6096e-04	-0.3884
chr19:58313312-58314617:+	PCPG	EHT.1864	EER	1.0951e-02	-0.4734
ENSG00000142396.9,ERVK3-1	PCPG	EHT.1864	EAG	1.0951e-02	-0.4734
chr19:58313312-58314617:+	PRAD	Imatinib	EER	2.4202e-02	-0.2444
ENSG00000142396.9,ERVK3-1	PRAD	Imatinib	EAG	2.4202e-02	-0.2444
chr19:58313312-58314617:+	STAD	GW.441756	EER	1.8249e-02	-0.1729
ENSG00000142396.9,ERVK3-1	STAD	GW.441756	EAG	2.2204e-02	-0.1676
ENSG00000142396.9,ERVK3-1	THCA	Bortezomib	EAG	2.4136e-03	-0.3078
chr19:58313312-58314617:+	UCS	AZD6244	EER	3.5262e-02	-0.4408
ENSG00000142396.9,ERVK3-1	UCS	AZD6244	EAG	3.5262e-02	-0.4408

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EAGs targeted by drugs from DrugBank database.

* EAG: EER-associated genes.

EER

ENST

UniprotID

DrugBankID

Drug

DrugType