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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: AFF1 (ImmuneEditome ID:4299)

1. Gene summary of enriched editing regions for AFF1

check button Gene summary
Gene informationGene symbol

AFF1

Gene ID

4299

GeneSynonymsAF4|FEL|MLLT2|PBM1
GeneCytomap

4q21.3-q22.1

GeneTypeprotein-coding
GeneDescriptionAF4/FMR2 family member 1|ALL1-fused gene from chromosome 4 protein|KMT2A/AFF1 fusion protein|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2|pre-B-cell monocytic leukemia partner 1|proto-oncogene AF4
GeneModificationdate20230329
UniprotIDP51825;Q14C88;D6RIZ5;E7EMC5;A0A669KBI3;H0Y9S4;D6RAU0;E7ETI4
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr4:86937594-86938420:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicAluJr,AluSzchr4:86937594-86938420:+.alignment
chr4:86937594-86938420:+ENST00000511996.4ENSG00000172493.19AFF1ncRNA_intronicAluJr,AluSzchr4:86937594-86938420:+.alignment
chr4:86969710-86969849:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicAluYk3chr4:86969710-86969849:+.alignment
chr4:86969710-86969849:+ENST00000511996.4ENSG00000172493.19AFF1ncRNA_intronicAluYk3chr4:86969710-86969849:+.alignment
chr4:86971902-86972720:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicMER33,AluSz6,AluJbchr4:86971902-86972720:+.alignment
chr4:86971902-86972720:+ENST00000511996.4ENSG00000172493.19AFF1ncRNA_intronicMER33,AluSz6,AluJbchr4:86971902-86972720:+.alignment
chr4:86982618-86983939:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicMLT1A0,AluSz,AluY,AluSp,AluSx1,Tigger6achr4:86982618-86983939:+.alignment
chr4:86986978-86987837:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicAluSz,AluJrchr4:86986978-86987837:+.alignment
chr4:86994945-86995161:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicAluJbchr4:86994945-86995161:+.alignment
chr4:86997097-86998053:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicAluY,AluSp,AluSx1,MSTCchr4:86997097-86998053:+.alignment
chr4:87022009-87023052:+ENST00000504956.4ENSG00000172493.19AFF1ncRNA_intronicAluJo,(AT)n,(TA)n,AluSx1,(TTTA)nchr4:87022009-87023052:+.alignment
chr4:87064744-87065008:+ENST00000307808.9ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment
chr4:87064744-87065008:+ENST00000395146.7ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment
chr4:87064744-87065008:+ENST00000503477.4ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment
chr4:87064744-87065008:+ENST00000507468.4ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment
chr4:87064744-87065008:+ENST00000511722.4ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment
chr4:87064744-87065008:+ENST00000514970.2ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment
chr4:87064744-87065008:+ENST00000544085.4ENSG00000172493.19AFF1intronicAluJb,AluSq2chr4:87064744-87065008:+.alignment


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2. Tumor-specific enriched editing regions for AFF1


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


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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 AFF1


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

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4. Enriched editing regions and immune related splicing for AFF1


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
ENSG00000172493.19,AFF1
ESCAEAGIRENSG00000132530.12chr176759840:6759881:6760405:6760479-0.35821.4797e-025.6878e-06-0.4511imageNADAR;CELF2;CSTF2T;DKC1;EIF4A3;ELAVL1;EWSR1;FAM120A;FUS;GTF2F1;HNRNPA1;HNRNPC;HNRNPK;HNRNPL;IGF2BP2;MSI2;PRPF8;PTBP1;RBFOX2;SF3B4;SRSF1;TAF15;TIA1;TROVE2;U2AF1;U2AF2XAF1EosinophilsGSVA_HALLMARK_UV_RESPONSE_UP
ENSG00000172493.19,AFF1
ESCAEAGA3ENSG00000101311.11chr206122773:6123030:6119420:6119575:6119420:6119734-0.26375.5687e-032.1252e-08-0.5114imageNACIN1;ADAR;ALYREF;AUH;BUD13;CSTF2T;DHX9;DKC1;EIF4A3;ELAVL1;FAM120A;FBL;FMR1;FUS;GTF2F1;HNRNPA1;HNRNPC;HNRNPK;HNRNPL;IGF2BP1;IGF2BP2;IGF2BP3;KHDRBS3;LIN28B;MOV10;NOP56;NOP58;PCBP2;PRPF8;PTBP1;QKI;RBFOX2;RBM10;RBM5;SF3A3;SF3B4;SLTM;SMNDC1;SND1;SRSF1;SRSF3;SRSF7;SRSF9;TAF15;TIA1;TIAL1;TRA2A;U2AF1;U2AF2;UPF1;YTHDC1;YTHDF1;YTHDF2FERMT1NK_cells_activatedGSVA_HALLMARK_ALLOGRAFT_REJECTION
ENSG00000172493.19,AFF1
ESCAEAGESENSG00000169045.13chr5179618238:179618323:179619268:179619360:179620891:1796209590.39032.4800e-026.6523e-060.4062imageNACIN1;ADAR;AIFM1;ALYREF;AUH;BCCIP;BUD13;CBX7;CELF2;CNBP;CPSF6;CSTF2T;DDX3X;DDX42;DDX54;DGCR8;DHX9;DICER1;DKC1;EIF4A3;EIF4G2;ELAVL1;ELAVL3;EWSR1;FAM120A;FBL;FMR1;FTO;FUS;FXR1;FXR2;GNL3;GTF2F1;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPD;HNRNPK;HNRNPL;HNRNPM;IGF2BP1;IGF2BP2;IGF2BP3;ILF3;KHDRBS1;KHDRBS2;KHDRBS3;KHSRP;LARP7;LIN28;LIN28A;LIN28B;LSM11;MBNL2;MOV10;MSI1;MSI2;NCBP3;NONO;NOP56;NOP58;NPM1;NUMA1;PCBP2;PRPF8;PTBP1;QKI;RANGAP1;RBFOX2;RBM10;RBM22;RBM27;RBM47;RBM5;RC3H1;RNF219;SAFB2;SBDS;SF3A3;SF3B4;SLBP;SLTM;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARBP2;TARDBP;TIA1;TIAL1;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;XRN2;YTHDC1;YTHDF1;YWHAG;ZC3H7B;ZNF184NADendritic_cells_activatedGSVA_HALLMARK_G2M_CHECKPOINT
ENSG00000172493.19,AFF1
ESCAEAGA3ENSG00000169045.13chr5179620891:179620959:179618144:179618323:179618144:179619360-0.39032.4800e-026.6523e-06-0.4062imageNACIN1;ADAR;AIFM1;ALYREF;AUH;BCCIP;BUD13;CBX7;CELF2;CNBP;CPSF6;CSTF2T;DDX3X;DDX42;DDX54;DGCR8;DHX9;DICER1;DKC1;EIF4A3;EIF4G2;ELAVL1;ELAVL3;EWSR1;FAM120A;FBL;FMR1;FTO;FUS;FXR1;FXR2;GNL3;GTF2F1;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPD;HNRNPK;HNRNPL;HNRNPM;IGF2BP1;IGF2BP2;IGF2BP3;ILF3;KHDRBS1;KHDRBS2;KHDRBS3;KHSRP;LARP7;LIN28;LIN28A;LIN28B;LSM11;MBNL2;MOV10;MSI1;MSI2;NCBP3;NONO;NOP56;NOP58;NPM1;NUMA1;PCBP2;PRPF8;PTBP1;QKI;RANGAP1;RBFOX2;RBM10;RBM22;RBM27;RBM47;RBM5;RC3H1;RNF219;SAFB2;SBDS;SF3A3;SF3B4;SLBP;SLTM;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARBP2;TARDBP;TIA1;TIAL1;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;XRN2;YTHDC1;YTHDF1;YWHAG;ZC3H7B;ZNF184NADendritic_cells_activatedGSVA_HALLMARK_G2M_CHECKPOINT

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5. Enriched editing regions and immune infiltration for AFF1


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
chr4:86997097-86998053:+ESCAEERB_cells_memory1.3073e-020.4478image
chr4:86971902-86972720:+LAMLEERMast_cells_activated2.4306e-020.3151image
ENSG00000172493.19,AFF1LAMLEAGT_cells_gamma_delta3.5296e-030.2459image
ENSG00000172493.19,AFF1LUADEAGT_cells_CD4_memory_activated2.0255e-020.3413image
chr4:86997097-86998053:+OVEERNK_cells_activated3.9913e-020.3595image
ENSG00000172493.19,AFF1OVEAGT_cells_follicular_helper1.8808e-020.2744image
ENSG00000172493.19,AFF1PRADEAGT_cells_gamma_delta3.8862e-02-0.3279image
chr4:86937594-86938420:+STADEERT_cells_CD4_memory_activated3.0674e-030.2588image
chr4:86971902-86972720:+STADEERDendritic_cells_resting4.9695e-02-0.1859image
chr4:86982618-86983939:+STADEERB_cells_memory9.1964e-03-0.3009image
chr4:86994945-86995161:+STADEERT_cells_regulatory_(Tregs)1.7537e-03-0.5033image
chr4:86997097-86998053:+STADEERNK_cells_activated3.0025e-02-0.2736image
chr4:87022009-87023052:+STADEERMacrophages_M22.7366e-030.3192image
ENSG00000172493.19,AFF1STADEAGPlasma_cells8.9828e-03-0.1778image
ENSG00000172493.19,AFF1TGCTEAGT_cells_CD4_memory_activated2.7201e-02-0.3093image
ENSG00000172493.19,AFF1THCAEAGMacrophages_M24.4882e-02-0.2096image


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6. Enriched editing regions and immune gene sets for AFF1


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
ENSG00000172493.19,AFF1BLCAGSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITIONEAG4.1632e-020.4280image
ENSG00000172493.19,AFF1BRCAGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG2.1219e-020.2387image
ENSG00000172493.19,AFF1CESCGSVA_HALLMARK_PEROXISOMEEAG3.6380e-020.4483image
ENSG00000172493.19,AFF1ESCAGSVA_HALLMARK_G2M_CHECKPOINTEAG2.1754e-030.2831image
chr4:86997097-86998053:+ESCAGSVA_HALLMARK_ANDROGEN_RESPONSEEER2.4767e-02-0.4091image
chr4:86982618-86983939:+ESCAGSVA_HALLMARK_MTORC1_SIGNALINGEER7.0193e-030.3503image
ENSG00000172493.19,AFF1KIRCGSVA_HALLMARK_DNA_REPAIREAG1.7424e-020.2652image
ENSG00000172493.19,AFF1LAMLGSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITIONEAG8.2357e-030.2233image
ENSG00000172493.19,AFF1LUADGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG2.1085e-030.4419image
ENSG00000172493.19,AFF1LUSCGSVA_HALLMARK_MITOTIC_SPINDLEEAG1.2909e-02-0.5327image
chr4:86982618-86983939:+OVGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER4.3366e-020.3713image
ENSG00000172493.19,AFF1PRADGSVA_HALLMARK_ANDROGEN_RESPONSEEAG8.5176e-030.4105image
chr4:86971902-86972720:+STADGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER1.7905e-040.3469image
chr4:86982618-86983939:+STADGSVA_HALLMARK_ADIPOGENESISEER5.2449e-060.5018image
chr4:86937594-86938420:+STADGSVA_HALLMARK_UV_RESPONSE_UPEER1.1970e-020.2207image
chr4:86994945-86995161:+STADGSVA_HALLMARK_P53_PATHWAYEER7.6857e-030.4371image
ENSG00000172493.19,AFF1STADGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG1.4758e-070.3491image
ENSG00000172493.19,AFF1TGCTGSVA_HALLMARK_HEME_METABOLISMEAG3.2918e-020.2992image
ENSG00000172493.19,AFF1THCAGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG3.4449e-03-0.3019image


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7. Enriched editing regions and drugs for AFF1


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
ENSG00000172493.19,AFF1BLCAAZD.2281EAG1.6673e-02-0.4936image
ENSG00000172493.19,AFF1CESCFH535EAG1.6096e-02-0.5067image
chr4:86997097-86998053:+ESCACyclopamineEER1.3418e-02-0.4464image
chr4:86982618-86983939:+ESCAFH535EER8.7248e-030.3414image
ENSG00000172493.19,AFF1KIRCImatinibEAG3.1527e-020.2407image
chr4:86971902-86972720:+LAMLAZD7762EER1.0321e-02-0.3561image
ENSG00000172493.19,AFF1LAMLAZD7762EAG1.1717e-02-0.2133image
ENSG00000172493.19,AFF1LUADBMS.708163EAG1.0670e-020.3730image
ENSG00000172493.19,AFF1OVDasatinibEAG4.2084e-030.3312image
chr4:86997097-86998053:+OVCHIR.99021EER2.9375e-020.3795image
chr4:86982618-86983939:+OVABT.888EER2.1136e-03-0.5391image
ENSG00000172493.19,AFF1PRADAZD.2281EAG5.5446e-030.4359image
chr4:86997097-86998053:+STADGefitinibEER4.8521e-04-0.4269image
chr4:86971902-86972720:+STADAG.014699EER1.2118e-020.2363image
chr4:87022009-87023052:+STADJNK.Inhibitor.VIIIEER2.4949e-020.2417image
chr4:86982618-86983939:+STADBX.795EER6.6648e-030.3128image
chr4:86937594-86938420:+STADAICAREER1.8515e-020.2071image
chr4:86994945-86995161:+STADAxitinibEER3.4042e-030.4752image
ENSG00000172493.19,AFF1STADBortezomibEAG3.0629e-03-0.2011image
ENSG00000172493.19,AFF1THCAMetforminEAG2.9993e-020.2264image


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