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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: UBE4B (ImmuneEditome ID:10277)

1. Gene summary of enriched editing regions for UBE4B

check button Gene summary
Gene informationGene symbol

UBE4B

Gene ID

10277

GeneSynonymsE4|HDNB1|UBOX3|UFD2|UFD2A
GeneCytomap

1p36.22

GeneTypeprotein-coding
GeneDescriptionubiquitin conjugation factor E4 B|RING-type E3 ubiquitin transferase E4 B|homologous to yeast UFD2|homozygously deleted in neuroblastoma-1|ubiquitin-fusion degradation protein 2|ubiquitination factor E4B (UFD2 homolog, yeast)
GeneModificationdate20230329
UniprotIDO95155;B1AQ61
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr1:10061345-10061517:+ENST00000253251.11ENSG00000130939.17UBE4BintronicAluSxchr1:10061345-10061517:+.alignment
chr1:10061345-10061517:+ENST00000343090.9ENSG00000130939.17UBE4BintronicAluSxchr1:10061345-10061517:+.alignment
chr1:10061345-10061517:+ENST00000377153.4ENSG00000130939.17UBE4BintronicAluSxchr1:10061345-10061517:+.alignment
chr1:10092113-10092822:+ENST00000253251.11ENSG00000130939.17UBE4BintronicAluSp,AluJo,AluSx4chr1:10092113-10092822:+.alignment
chr1:10092113-10092822:+ENST00000343090.9ENSG00000130939.17UBE4BintronicAluSp,AluJo,AluSx4chr1:10092113-10092822:+.alignment
chr1:10111698-10112614:+ENST00000475795.4ENSG00000130939.17UBE4BncRNA_intronicKanga11a,AluSx1,AluSzchr1:10111698-10112614:+.alignment
chr1:10113909-10114792:+ENST00000475795.4ENSG00000130939.17UBE4BncRNA_intronicAluSz,AluSc,Kanga11achr1:10113909-10114792:+.alignment
chr1:10123133-10123872:+ENST00000475795.4ENSG00000130939.17UBE4BncRNA_intronicAluSq2,L1MB5,(TGTT)n,(TTGTT)n,AluSx1chr1:10123133-10123872:+.alignment
chr1:10143491-10144621:+ENST00000466379.1ENSG00000130939.17UBE4BncRNA_intronicMLT1D,MER104,L2a,(TCAGCC)n,AluSx3,LTR67Bchr1:10143491-10144621:+.alignment
chr1:10154122-10154792:+ENST00000253251.11ENSG00000130939.17UBE4BintronicAluSx,AluSc,AluSq2,LTR50,L1ME4achr1:10154122-10154792:+.alignment
chr1:10154122-10154792:+ENST00000343090.9ENSG00000130939.17UBE4BintronicAluSx,AluSc,AluSq2,LTR50,L1ME4achr1:10154122-10154792:+.alignment
chr1:10156254-10157698:+ENST00000253251.11ENSG00000130939.17UBE4BintronicAluSz6,AluJr,AluSc,AluJbchr1:10156254-10157698:+.alignment
chr1:10156254-10157698:+ENST00000343090.9ENSG00000130939.17UBE4BintronicAluSz6,AluJr,AluSc,AluJbchr1:10156254-10157698:+.alignment
chr1:10163952-10164516:+ENST00000253251.11ENSG00000130939.17UBE4Bintronic(TTA)n,AluJr,AluSz6,AluSx1chr1:10163952-10164516:+.alignment
chr1:10163952-10164516:+ENST00000343090.9ENSG00000130939.17UBE4Bintronic(TTA)n,AluJr,AluSz6,AluSx1chr1:10163952-10164516:+.alignment
chr1:10163952-10164516:+ENST00000488228.1ENSG00000130939.17UBE4Bintronic(TTA)n,AluJr,AluSz6,AluSx1chr1:10163952-10164516:+.alignment
chr1:10166477-10166831:+ENST00000253251.11ENSG00000130939.17UBE4BintronicAluSz,AluSxchr1:10166477-10166831:+.alignment
chr1:10166477-10166831:+ENST00000343090.9ENSG00000130939.17UBE4BintronicAluSz,AluSxchr1:10166477-10166831:+.alignment
chr1:10166477-10166831:+ENST00000488228.1ENSG00000130939.17UBE4BintronicAluSz,AluSxchr1:10166477-10166831:+.alignment


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2. Tumor-specific enriched editing regions for UBE4B


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 UBE4B


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 UBE4B


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
ENSG00000130939.17,UBE4B
ESCAEAGMEXENSG00000129657.10chr1777215553:77215753:77215792:77215805:77215818:77215883:77215997:77216010-0.30401.1540e-023.7548e-06-0.4358imageNACIN1;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;HNRNPK;HNRNPL;HNRNPM;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;IGF2BP3;ILF3;KHDRBS1;KHDRBS2;KHDRBS3;KHSRP;LARP7;LIN28;LIN28A;LIN28B;MBNL2;MOV10;MSI1;MSI2;NONO;NOP56;NOP58;NPM1;NUMA1;PCBP2;PRPF8;PTBP1;QKI;RANGAP1;RBFOX2;RBM10;RBM22;RBM47;RNF219;RTCB;SAFB2;SF3A3;SF3B4;SLBP;SLTM;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARBP2;TARDBP;TIA1;TIAL1;TNRC6A;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;VIM;WTAP;XRN2;YTHDC1;YTHDF1;YWHAG;ZC3H7B;ZNF184NAT_cells_CD4_memory_resting
ENSG00000130939.17,UBE4B
ESCAEAGMEXENSG00000129657.10chr1777215553:77215753:77215792:77215818:77215818:77215883:77215997:77216010-0.30401.1540e-023.7548e-06-0.4358imageNACIN1;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;HNRNPK;HNRNPL;HNRNPM;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;IGF2BP3;ILF3;KHDRBS1;KHDRBS2;KHDRBS3;KHSRP;LARP7;LIN28;LIN28A;LIN28B;MBNL2;MOV10;MSI1;MSI2;NONO;NOP56;NOP58;NPM1;NUMA1;PCBP2;PRPF8;PTBP1;QKI;RANGAP1;RBFOX2;RBM10;RBM22;RBM47;RNF219;RTCB;SAFB2;SF3A3;SF3B4;SLBP;SLTM;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARBP2;TARDBP;TIA1;TIAL1;TNRC6A;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;VIM;WTAP;XRN2;YTHDC1;YTHDF1;YWHAG;ZC3H7B;ZNF184NAT_cells_CD4_memory_resting

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5. Enriched editing regions and immune infiltration for UBE4B


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
chr1:10111698-10112614:+ESCAEERT_cells_regulatory_(Tregs)1.3002e-02-0.3943image
chr1:10163952-10164516:+ESCAEEREosinophils2.3996e-02-0.2433image
ENSG00000130939.17,UBE4BESCAEAGMonocytes8.4357e-03-0.2467image
ENSG00000130939.17,UBE4BLAMLEAGDendritic_cells_resting2.4891e-020.1930image
ENSG00000130939.17,UBE4BOVEAGMacrophages_M12.8542e-030.3293image
chr1:10123133-10123872:+STADEERB_cells_memory1.0151e-030.5697image
ENSG00000130939.17,UBE4BSTADEAGMast_cells_activated4.6700e-020.1493image
ENSG00000130939.17,UBE4BTHCAEAGPlasma_cells6.8952e-040.5935image


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6. Enriched editing regions and immune gene sets for UBE4B


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
ENSG00000130939.17,UBE4BBRCAGSVA_HALLMARK_NOTCH_SIGNALINGEAG3.4116e-060.8410image
chr1:10111698-10112614:+ESCAGSVA_HALLMARK_E2F_TARGETSEER1.8728e-020.3748image
chr1:10143491-10144621:+ESCAGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER2.2438e-02-0.2688image
chr1:10163952-10164516:+LAMLGSVA_HALLMARK_MYC_TARGETS_V2EER2.9211e-020.3218image
ENSG00000130939.17,UBE4BLAMLGSVA_HALLMARK_MYC_TARGETS_V2EAG8.3130e-030.2263image
ENSG00000130939.17,UBE4BLIHCGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG2.5758e-02-0.4285image
ENSG00000130939.17,UBE4BOVGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG8.1311e-050.4261image
ENSG00000130939.17,UBE4BSTADGSVA_HALLMARK_PEROXISOMEEAG3.1947e-040.2667image
chr1:10163952-10164516:+STADGSVA_HALLMARK_UV_RESPONSE_UPEER2.1061e-030.2634image
chr1:10092113-10092822:+STADGSVA_HALLMARK_MYC_TARGETS_V1EER4.1909e-030.3455image
chr1:10111698-10112614:+STADGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEER6.8615e-030.2862image
ENSG00000130939.17,UBE4BTHCAGSVA_HALLMARK_ANDROGEN_RESPONSEEAG2.4502e-02-0.4168image


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7. Enriched editing regions and drugs for UBE4B


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
ENSG00000130939.17,UBE4BBRCAABT.888EAG1.4818e-030.6618image
chr1:10163952-10164516:+ESCAA.770041EER2.9110e-02-0.2354image
ENSG00000130939.17,UBE4BESCABMS.708163EAG8.6770e-04-0.3090image
chr1:10163952-10164516:+LAMLBMS.708163EER2.0189e-030.4436image
ENSG00000130939.17,UBE4BLAMLAZD.2281EAG2.3942e-02-0.1943image
ENSG00000130939.17,UBE4BOVGSK.650394EAG1.3765e-030.3518image
ENSG00000130939.17,UBE4BSTADLenalidomideEAG2.1178e-020.1727image
chr1:10163952-10164516:+STADAG.014699EER7.9172e-040.2865image
chr1:10092113-10092822:+STADMG.132EER3.8580e-03-0.3484image
chr1:10111698-10112614:+STADAP.24534EER1.0766e-020.2706image
chr1:10166477-10166831:+STADGefitinibEER4.7052e-04-0.6950image
ENSG00000130939.17,UBE4BTHCALapatinibEAG1.1892e-050.7174image


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