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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: PAM16 (ImmuneEditome ID:51025)

1. Gene summary of enriched editing regions for PAM16

Gene summary

Gene information	Gene symbol	PAM16
	Gene ID	51025
	GeneSynonyms	CGI-136\|MAGMAS\|SMDMDM\|TIM16\|TIMM16
	GeneCytomap	16p13.3
	GeneType	protein-coding
	GeneDescription	mitochondrial import inner membrane translocase subunit TIM16\|magmas-like protein\|mitochondria associated protein involved in granulocyte macrophage colony stimulating factor signal transduction\|mitochondria-associated granulocyte macrophage CSF-signaling molecule\|presequence translocase associated motor 16 homolog
	GeneModificationdate	20230329
	UniprotID	Q9Y3D7;I3L0X9;A0A0B4J298;I3L1K9;I3L1U7;I3L3T0
	PubMed ID

UCSC image.

Locations of each EERs.

EER	ENST	ENSG	GeneName	Region	Repeat	dsRNA structure
chr16:4348703-4350614:-	ENST00000573614.4	ENSG00000217930.6	PAM16	ncRNA_intronic	AluJb,AluSx3,AluSz6,AluJo,(TA)n,MER5A,MIRb,AluY	chr16:4348703-4350614:-.alignment
chr16:4348703-4350614:-	ENST00000575942.1	ENSG00000217930.6	PAM16	ncRNA_intronic	AluJb,AluSx3,AluSz6,AluJo,(TA)n,MER5A,MIRb,AluY	chr16:4348703-4350614:-.alignment

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2. Tumor-specific enriched editing regions for PAM16

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	P	R	Boxplot
chr16:4348703-4350614:-	STAD	Path	EER	4.9520e-02	4.9131e-02	0.1393
ENSG00000217930.6,PAM16	STAD	Path	EAG	3.4197e-02	3.9639e-02	0.1449

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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
chr16:4348703-4350614:-	BRCA	EER	2.6484e-02	2.8846e-02	3.2016e-02
chr16:4348703-4350614:-	LUAD	EER	4.3186e-02	3.3392e-02	1.0066e+01
ENSG00000217930.6,PAM16	LUAD	EAG	4.4269e-02	3.8241e-02	9.0967e+00

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3. Enriched editing regions and immune related genes for PAM16

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 PAM16

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 PAM16

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
ENSG00000217930.6,PAM16	BRCA	EAG	Plasma_cells	2.9152e-02	0.1406
chr16:4348703-4350614:-	CESC	EER	Dendritic_cells_activated	1.5201e-02	0.3485
ENSG00000217930.6,PAM16	CESC	EAG	Dendritic_cells_activated	1.5201e-02	0.3485
ENSG00000217930.6,PAM16	COAD	EAG	Eosinophils	2.5903e-02	0.3934
chr16:4348703-4350614:-	ESCA	EER	Macrophages_M2	6.4053e-03	0.2696
ENSG00000217930.6,PAM16	ESCA	EAG	Macrophages_M2	9.1600e-03	0.2569
chr16:4348703-4350614:-	KIRC	EER	Dendritic_cells_activated	1.0967e-03	0.3521
ENSG00000217930.6,PAM16	KIRC	EAG	Dendritic_cells_activated	2.3716e-09	0.5894
chr16:4348703-4350614:-	LAML	EER	Macrophages_M2	6.4921e-03	-0.2394
ENSG00000217930.6,PAM16	LAML	EAG	Plasma_cells	1.7565e-02	0.2080
chr16:4348703-4350614:-	LIHC	EER	Macrophages_M0	4.5110e-03	0.3379
ENSG00000217930.6,PAM16	LIHC	EAG	Macrophages_M0	4.5110e-03	0.3379
chr16:4348703-4350614:-	LUSC	EER	Dendritic_cells_resting	7.2399e-03	0.3491
ENSG00000217930.6,PAM16	LUSC	EAG	Dendritic_cells_resting	8.3456e-03	0.3404
chr16:4348703-4350614:-	OV	EER	T_cells_regulatory_(Tregs)	4.1829e-02	0.1601
ENSG00000217930.6,PAM16	OV	EAG	T_cells_regulatory_(Tregs)	4.1103e-02	0.1602
ENSG00000217930.6,PAM16	SARC	EAG	Plasma_cells	1.1200e-04	0.6959
chr16:4348703-4350614:-	SKCM	EER	T_cells_regulatory_(Tregs)	3.9730e-02	0.2538
ENSG00000217930.6,PAM16	SKCM	EAG	T_cells_regulatory_(Tregs)	3.8207e-02	0.2538
chr16:4348703-4350614:-	STAD	EER	T_cells_CD8	4.3885e-03	0.1972
ENSG00000217930.6,PAM16	STAD	EAG	T_cells_CD8	3.1109e-03	0.2036

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6. Enriched editing regions and immune gene sets for PAM16

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
ENSG00000217930.6,PAM16	BLCA	GSVA_HALLMARK_MYC_TARGETS_V2	EAG	2.1324e-02	-0.2691
chr16:4348703-4350614:-	BLCA	GSVA_HALLMARK_MYC_TARGETS_V2	EER	2.1286e-02	-0.2710
chr16:4348703-4350614:-	BRCA	GSVA_HALLMARK_XENOBIOTIC_METABOLISM	EER	3.1534e-02	-0.1397
ENSG00000217930.6,PAM16	CESC	GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS	EAG	2.9729e-02	-0.3140
chr16:4348703-4350614:-	CESC	GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS	EER	2.9729e-02	-0.3140
ENSG00000217930.6,PAM16	COAD	GSVA_HALLMARK_SPERMATOGENESIS	EAG	4.8746e-03	-0.4853
chr16:4348703-4350614:-	ESCA	GSVA_HALLMARK_HYPOXIA	EER	1.2160e-02	0.2487
ENSG00000217930.6,PAM16	ESCA	GSVA_HALLMARK_HYPOXIA	EAG	2.5307e-02	0.2214
ENSG00000217930.6,PAM16	KIRC	GSVA_HALLMARK_P53_PATHWAY	EAG	6.2747e-03	-0.2925
chr16:4348703-4350614:-	KIRC	GSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKB	EER	3.2954e-02	-0.2344
ENSG00000217930.6,PAM16	KIRP	GSVA_HALLMARK_UV_RESPONSE_DN	EAG	4.3362e-02	0.3386
chr16:4348703-4350614:-	KIRP	GSVA_HALLMARK_UV_RESPONSE_DN	EER	4.3362e-02	0.3386
ENSG00000217930.6,PAM16	LIHC	GSVA_HALLMARK_PROTEIN_SECRETION	EAG	2.4671e-02	0.2703
chr16:4348703-4350614:-	LIHC	GSVA_HALLMARK_PROTEIN_SECRETION	EER	2.4671e-02	0.2703
chr16:4348703-4350614:-	LUAD	GSVA_HALLMARK_APICAL_JUNCTION	EER	4.0000e-02	-0.1927
ENSG00000217930.6,PAM16	LUAD	GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS	EAG	4.6087e-02	0.1856
chr16:4348703-4350614:-	LUSC	GSVA_HALLMARK_TGF_BETA_SIGNALING	EER	1.5127e-02	0.3176
ENSG00000217930.6,PAM16	LUSC	GSVA_HALLMARK_TGF_BETA_SIGNALING	EAG	1.4033e-02	0.3182
chr16:4348703-4350614:-	OV	GSVA_HALLMARK_PANCREAS_BETA_CELLS	EER	7.0462e-04	0.2635
ENSG00000217930.6,PAM16	OV	GSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY	EAG	9.2776e-04	0.2570
ENSG00000217930.6,PAM16	PAAD	GSVA_HALLMARK_MITOTIC_SPINDLE	EAG	4.8541e-02	0.3572
ENSG00000217930.6,PAM16	SARC	GSVA_HALLMARK_IL2_STAT5_SIGNALING	EAG	2.8812e-02	0.4373
chr16:4348703-4350614:-	SKCM	GSVA_HALLMARK_IL2_STAT5_SIGNALING	EER	2.8654e-02	0.2695
ENSG00000217930.6,PAM16	SKCM	GSVA_HALLMARK_IL2_STAT5_SIGNALING	EAG	2.7993e-02	0.2686
chr16:4348703-4350614:-	STAD	GSVA_HALLMARK_KRAS_SIGNALING_DN	EER	2.2882e-06	0.3217
ENSG00000217930.6,PAM16	STAD	GSVA_HALLMARK_KRAS_SIGNALING_DN	EAG	2.7450e-06	0.3178

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7. Enriched editing regions and drugs for PAM16

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
ENSG00000217930.6,PAM16	BLCA	Docetaxel	EAG	3.7014e-03	0.3356
chr16:4348703-4350614:-	BLCA	Docetaxel	EER	4.1089e-03	0.3343
chr16:4348703-4350614:-	BRCA	Docetaxel	EER	2.2310e-03	0.1977
ENSG00000217930.6,PAM16	BRCA	CEP.701	EAG	2.0228e-02	0.1495
ENSG00000217930.6,PAM16	CESC	AKT.inhibitor.VIII	EAG	3.9904e-02	-0.2977
chr16:4348703-4350614:-	CESC	AKT.inhibitor.VIII	EER	3.9904e-02	-0.2977
ENSG00000217930.6,PAM16	COAD	Cyclopamine	EAG	1.5582e-02	0.4307
chr16:4348703-4350614:-	ESCA	FH535	EER	9.8921e-03	0.2556
ENSG00000217930.6,PAM16	ESCA	FH535	EAG	7.7815e-03	0.2621
ENSG00000217930.6,PAM16	KIRC	BI.D1870	EAG	6.9613e-08	0.5422
chr16:4348703-4350614:-	KIRC	BI.D1870	EER	5.9095e-05	0.4261
ENSG00000217930.6,PAM16	KIRP	GDC.0449	EAG	3.3808e-02	-0.3546
chr16:4348703-4350614:-	KIRP	GDC.0449	EER	3.3808e-02	-0.3546
chr16:4348703-4350614:-	LAML	Cisplatin	EER	4.4276e-03	-0.2500
ENSG00000217930.6,PAM16	LAML	Elesclomol	EAG	2.8740e-03	-0.2595
ENSG00000217930.6,PAM16	LIHC	Etoposide	EAG	1.5471e-04	0.4400
chr16:4348703-4350614:-	LIHC	Etoposide	EER	1.5471e-04	0.4400
chr16:4348703-4350614:-	LUAD	BX.795	EER	4.1750e-03	0.2664
ENSG00000217930.6,PAM16	LUAD	BX.795	EAG	2.4100e-02	0.2094
chr16:4348703-4350614:-	LUSC	CGP.60474	EER	1.0239e-02	0.3346
ENSG00000217930.6,PAM16	LUSC	AZD7762	EAG	1.2696e-02	0.3226
chr16:4348703-4350614:-	OV	GNF.2	EER	4.0925e-04	-0.2744
ENSG00000217930.6,PAM16	OV	GNF.2	EAG	6.2949e-04	-0.2650
ENSG00000217930.6,PAM16	PAAD	FTI.277	EAG	2.2338e-02	-0.4090
ENSG00000217930.6,PAM16	SARC	FTI.277	EAG	8.2206e-05	0.7053
chr16:4348703-4350614:-	SKCM	AMG.706	EER	8.6456e-04	-0.4004
ENSG00000217930.6,PAM16	SKCM	AMG.706	EAG	9.6277e-04	-0.3942
chr16:4348703-4350614:-	STAD	BIRB.0796	EER	2.0281e-03	-0.2133
ENSG00000217930.6,PAM16	STAD	BIRB.0796	EAG	1.2527e-03	-0.2217

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EAGs targeted by drugs from DrugBank database.

* EAG: EER-associated genes.

EER

ENST

UniprotID

DrugBankID

Drug

DrugType