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Center for Computational Systems Medicine
Soverview

1. Gene summary of enriched editing regions

Soverview

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.

Soverview

3. Enriched editing regions and immune related genes

Soverview

4. Enriched editing regions and immune related splicing

Soverview

5. Enriched editing regions and immune infiltration

Soverview

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.

Soverview

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: AFG3L1P (ImmuneEditome ID:172)

1. Gene summary of enriched editing regions for AFG3L1P

check button Gene summary
Gene informationGene symbol

AFG3L1P

Gene ID

172

GeneSynonymsAFG3|AFG3L1
GeneCytomap

16q24.3

GeneTypepseudo
GeneDescriptionAFG3 (ATPase family gene 3, yeast)-like 1|AFG3 ATPase family gene 3-like 1, pseudogene|AFG3 ATPase family member 3-like 1, pseudogene|AFG3 like AAA ATPase 1, pseudogene
GeneModificationdate20230329
UniprotID.
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr16:89976257-89977279:+ENST00000418696.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000421164.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000423742.1ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000429663.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000431757.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000436447.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000437774.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000450026.1ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000457926.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89976257-89977279:+ENST00000557444.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSx1,AluSxchr16:89976257-89977279:+.alignment
chr16:89980829-89981110:+ENST00000388970.6ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000418696.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000421164.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000421780.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000423684.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000429663.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000436447.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000437774.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000457926.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000458301.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89980829-89981110:+ENST00000557444.4ENSG00000223959.7AFG3L1PncRNA_intronicAluJbchr16:89980829-89981110:+.alignment
chr16:89984938-89985171:+ENST00000388970.6ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89984938-89985171:+ENST00000418696.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89984938-89985171:+ENST00000436447.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89984938-89985171:+ENST00000437774.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89984938-89985171:+ENST00000457926.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89984938-89985171:+ENST00000458301.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89984938-89985171:+ENST00000557444.4ENSG00000223959.7AFG3L1PncRNA_intronicAluSzchr16:89984938-89985171:+.alignment
chr16:89987882-89988513:+ENST00000355531.6ENSG00000223959.7AFG3L1PncRNA_exonicAluJo,AluJr4,AluJbchr16:89987882-89988513:+.alignment


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2. Tumor-specific enriched editing regions for AFG3L1P


all structure

check buttonComparison of enriched editing regions between tumor and normal.
* P<0.05 and Informative number >=20.
* EER: enriched editing region, EAG: EER-associated genes.
ID_eventscancerTypePBoxplot


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check buttonCorrelation 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_eventscancerTypeStageTypeAnovaPPRBoxplot
ENSG00000223959.7,AFG3L1POVCliEAG8.3384e-039.4149e-040.2785image
chr16:89987882-89988513:+STADPathEER1.6518e-023.1130e-020.1829image


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check button Associations of enriched editing regions with cancer survival.
* Pkm<0.05 and Pcox<0.05.
* EER: enriched editing region, EAG: EER-associated genes.
ID_eventscancerTypeIDPkmPcox_continuousHR_continuousKMPlot

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3. Enriched editing regions and immune related genes for AFG3L1P


all structure

check button 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_eventscancerTypeGenebetaFDRPearsonPPearsonRCorrelationPlotRBPRBPtargetsImmuneGeneImmuneFractionHallMark

More results



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4. Enriched editing regions and immune related splicing for AFG3L1P


all structure

check button 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_eventscancerTypeSplicingTypeSplicingGeneSplicingChrSplicingPositionbetaFDRPearsonPPearsonRCorrelationPlotRBPRBPtargetsImmuneGeneImmuneFractionHallMark

More results



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5. Enriched editing regions and immune infiltration for AFG3L1P


all structure

check button 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_eventscancerTypeIDImmuneCellPRCorrelationPlot
ENSG00000223959.7,AFG3L1PBLCAEAGDendritic_cells_resting1.2065e-020.3304image
chr16:89984938-89985171:+BRCAEERMonocytes2.0151e-02-0.3380image
chr16:89987882-89988513:+BRCAEERMast_cells_resting2.1748e-030.2429image
ENSG00000223959.7,AFG3L1PCESCEAGNeutrophils3.0413e-030.3517image
ENSG00000223959.7,AFG3L1PCOADEAGDendritic_cells_activated1.7340e-020.3352image
chr16:89987882-89988513:+ESCAEERT_cells_regulatory_(Tregs)6.9033e-03-0.2539image
ENSG00000223959.7,AFG3L1PESCAEAGPlasma_cells2.2891e-020.1936image
chr16:89984938-89985171:+KIRCEERDendritic_cells_activated1.0477e-040.7589image
chr16:89987882-89988513:+KIRCEERT_cells_CD85.1867e-050.4290image
ENSG00000223959.7,AFG3L1PKIRCEAGT_cells_CD82.6988e-040.3833image
ENSG00000223959.7,AFG3L1PKIRPEAGMacrophages_M21.0708e-02-0.3327image
chr16:89987882-89988513:+LAMLEERB_cells_naive2.7570e-020.2298image
ENSG00000223959.7,AFG3L1PLAMLEAGB_cells_naive2.0867e-020.2221image
chr16:89987882-89988513:+LUADEERDendritic_cells_resting1.2299e-020.2251image
ENSG00000223959.7,AFG3L1PLUADEAGDendritic_cells_resting5.6360e-030.2434image
chr16:89987882-89988513:+LUSCEERMacrophages_M12.0420e-020.2305image
ENSG00000223959.7,AFG3L1PLUSCEAGMacrophages_M11.5816e-020.2328image
chr16:89987882-89988513:+PCPGEERMacrophages_M28.7093e-04-0.6234image
ENSG00000223959.7,AFG3L1PPCPGEAGMacrophages_M29.8447e-04-0.6184image
chr16:89976257-89977279:+STADEERT_cells_CD4_memory_activated5.2055e-030.3328image
chr16:89987882-89988513:+STADEERT_cells_CD4_memory_resting2.1859e-020.1916image
ENSG00000223959.7,AFG3L1PSTADEAGNK_cells_activated1.6788e-02-0.1549image


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6. Enriched editing regions and immune gene sets for AFG3L1P


all structure

check button 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_eventscancerTypeE2M_PBoxplotCorPCorRCorrelationPlot


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check button 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_eventscancerTypeBuffa_P Buffa_R Ragnum_P Ragnum_R Winter_P Winter_R HALLMARK_P HALLMARK_R CorrelationPlot


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check button 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_eventscancerHallmarkTypeTypePRCorrelationPlot
chr16:89987882-89988513:+BLCAGSVA_HALLMARK_APICAL_SURFACEEER3.8207e-030.3872image
ENSG00000223959.7,AFG3L1PBLCAGSVA_HALLMARK_APICAL_SURFACEEAG3.6654e-030.3788image
chr16:89987882-89988513:+BRCAGSVA_HALLMARK_BILE_ACID_METABOLISMEER3.3354e-030.2329image
ENSG00000223959.7,AFG3L1PBRCAGSVA_HALLMARK_BILE_ACID_METABOLISMEAG2.6499e-030.2240image
chr16:89984938-89985171:+BRCAGSVA_HALLMARK_SPERMATOGENESISEER1.3399e-020.3583image
ENSG00000223959.7,AFG3L1PCESCGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEAG3.8193e-030.3438image
ENSG00000223959.7,AFG3L1PCOADGSVA_HALLMARK_FATTY_ACID_METABOLISMEAG3.5789e-02-0.2976image
chr16:89987882-89988513:+ESCAGSVA_HALLMARK_P53_PATHWAYEER4.3407e-030.2676image
chr16:89987882-89988513:+GBMGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEER3.0566e-040.5418image
ENSG00000223959.7,AFG3L1PGBMGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG3.0469e-030.4515image
chr16:89984938-89985171:+KIRCGSVA_HALLMARK_APICAL_SURFACEEER2.6057e-040.7297image
chr16:89987882-89988513:+KIRCGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER1.3679e-060.5015image
ENSG00000223959.7,AFG3L1PKIRCGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG6.2251e-050.4180image
chr16:89987882-89988513:+KIRPGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEER5.3353e-040.4558image
ENSG00000223959.7,AFG3L1PKIRPGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEAG1.0550e-030.4192image
ENSG00000223959.7,AFG3L1PLAMLGSVA_HALLMARK_MYC_TARGETS_V2EAG2.6454e-020.2136image
chr16:89987882-89988513:+LGGGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEER3.6882e-020.2090image
ENSG00000223959.7,AFG3L1PLUADGSVA_HALLMARK_PROTEIN_SECRETIONEAG4.3733e-030.2503image
chr16:89987882-89988513:+LUADGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER1.8519e-03-0.2780image
chr16:89987882-89988513:+LUSCGSVA_HALLMARK_APOPTOSISEER8.3147e-040.3274image
ENSG00000223959.7,AFG3L1PLUSCGSVA_HALLMARK_APOPTOSISEAG1.6737e-030.3003image
ENSG00000223959.7,AFG3L1POVGSVA_HALLMARK_COAGULATIONEAG2.5252e-030.2815image
chr16:89987882-89988513:+PCPGGSVA_HALLMARK_UV_RESPONSE_UPEER8.7330e-030.5130image
ENSG00000223959.7,AFG3L1PPCPGGSVA_HALLMARK_UV_RESPONSE_UPEAG7.8621e-030.5189image
chr16:89987882-89988513:+SKCMGSVA_HALLMARK_ANDROGEN_RESPONSEEER3.0477e-02-0.2796image
ENSG00000223959.7,AFG3L1PSTADGSVA_HALLMARK_PROTEIN_SECRETIONEAG8.0293e-080.3393image
chr16:89987882-89988513:+STADGSVA_HALLMARK_HYPOXIAEER1.9868e-020.1946image
chr16:89987882-89988513:+TGCTGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEER2.9461e-020.3082image
ENSG00000223959.7,AFG3L1PTGCTGSVA_HALLMARK_UV_RESPONSE_UPEAG4.0915e-020.2902image
chr16:89987882-89988513:+THCAGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER8.2620e-030.3225image
ENSG00000223959.7,AFG3L1PTHCAGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG3.3448e-020.2476image


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7. Enriched editing regions and drugs for AFG3L1P


all structure

check button 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_eventscancerDrugTypePRCorrelationPlot
chr16:89987882-89988513:+BLCACyclopamineEER3.7863e-02-0.2834image
ENSG00000223959.7,AFG3L1PBLCACyclopamineEAG2.7245e-02-0.2925image
chr16:89987882-89988513:+BRCALapatinibEER4.7085e-04-0.2767image
ENSG00000223959.7,AFG3L1PBRCALapatinibEAG3.3449e-04-0.2666image
ENSG00000223959.7,AFG3L1PCESCGNF.2EAG2.4616e-04-0.4278image
ENSG00000223959.7,AFG3L1PCOADGW843682XEAG2.0968e-040.5012image
chr16:89987882-89988513:+ESCABMS.708163EER1.7382e-03-0.2927image
ENSG00000223959.7,AFG3L1PESCAGNF.2EAG4.3104e-02-0.1725image
chr16:89987882-89988513:+GBMBosutinibEER1.3198e-040.5680image
ENSG00000223959.7,AFG3L1PGBMAKT.inhibitor.VIIIEAG1.5595e-03-0.4783image
chr16:89984938-89985171:+KIRCAZD.2281EER8.4800e-05-0.7652image
chr16:89987882-89988513:+KIRCCGP.082996EER4.1195e-05-0.4342image
ENSG00000223959.7,AFG3L1PKIRCA.770041EAG2.8035e-06-0.4807image
chr16:89987882-89988513:+KIRPLFM.A13EER3.5763e-03-0.3898image
ENSG00000223959.7,AFG3L1PKIRPAZD.0530EAG2.4688e-03-0.3901image
chr16:89987882-89988513:+LGGABT.263EER2.5043e-030.2991image
ENSG00000223959.7,AFG3L1PLGGABT.263EAG4.5207e-030.2712image
ENSG00000223959.7,AFG3L1PLUADATRAEAG3.2422e-020.1892image
chr16:89987882-89988513:+LUADAZD7762EER4.8168e-020.1785image
chr16:89987882-89988513:+LUSCCisplatinEER5.3999e-04-0.3383image
ENSG00000223959.7,AFG3L1PLUSCCisplatinEAG2.3784e-04-0.3482image
chr16:89987882-89988513:+PCPGABT.888EER1.4859e-030.6010image
ENSG00000223959.7,AFG3L1PPCPGABT.888EAG1.4271e-030.6028image
chr16:89987882-89988513:+SKCMCEP.701EER3.1299e-03-0.3753image
ENSG00000223959.7,AFG3L1PSKCMCEP.701EAG8.6784e-03-0.3182image
ENSG00000223959.7,AFG3L1PSTADBI.2536EAG9.4587e-070.3115image
chr16:89976257-89977279:+STADAZD6244EER9.9809e-05-0.4512image
chr16:89987882-89988513:+STADBexaroteneEER2.6593e-03-0.2495image
chr16:89987882-89988513:+TGCTErlotinibEER1.0210e-02-0.3601image
ENSG00000223959.7,AFG3L1PTGCTErlotinibEAG1.1179e-02-0.3560image
chr16:89987882-89988513:+THCACI.1040EER7.3360e-04-0.4054image
ENSG00000223959.7,AFG3L1PTHCACisplatinEAG2.6514e-03-0.3445image


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check button EAGs targeted by drugs from DrugBank database.
* EAG: EER-associated genes.
EERENSTUniprotIDDrugBankIDDrugDrugType