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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: ZNF439 (ImmuneEditome ID:90594)

1. Gene summary of enriched editing regions for ZNF439

check button Gene summary
Gene informationGene symbol

ZNF439

Gene ID

90594

GeneSynonyms-
GeneCytomap

19p13.2

GeneTypeprotein-coding
GeneDescriptionzinc finger protein 439
GeneModificationdate20230518
UniprotIDQ8NDP4;A0A804HI69;A0A0C4DG37;C9JMA7
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr19:11850726-11850933:+ENST00000592495.1ENSG00000171291.7ZNF439ncRNA_exonicAluSz,MER41Dchr19:11850726-11850933:+.alignment
chr19:11852565-11853072:+ENST00000592534.1ENSG00000171291.7ZNF439ncRNA_intronicAluSz,AluSq4,MER57E3chr19:11852565-11853072:+.alignment
chr19:11864379-11865956:+ENST00000592534.1ENSG00000171291.7ZNF439ncRNA_intronicAluSz,MER68B,LTR60,(A)n,L1MB2,AluSpchr19:11864379-11865956:+.alignment
chr19:11869663-11870596:+ENST00000592534.1ENSG00000171291.7ZNF439ncRNA_intronicMER90a,(TTTAAT)n,AluSq2,AluSx3chr19:11869663-11870596:+.alignment


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2. Tumor-specific enriched editing regions for ZNF439


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
chr19:11869663-11870596:+BRCAPathEER1.9872e-021.6760e-030.1813image
ENSG00000171291.7,ZNF439BRCAPathEAG1.7811e-021.4702e-030.1793image


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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
chr19:11869663-11870596:+SARCEER7.5281e-033.2911e-024.7348e+01image
ENSG00000171291.7,ZNF439SARCEAG1.4219e-023.7414e-024.1205e+01image

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3. Enriched editing regions and immune related genes for ZNF439


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
chr19:11869663-11870596:+GBMEERENSG00000137494,ANKRD420.34645.4193e-031.1665e-060.4128imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_UV_RESPONSE_DN
chr19:11869663-11870596:+GBMEERENSG00000131711,MAP1B0.28143.6253e-021.1899e-060.4125imageNNNANK_cells_restingGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLY
chr19:11869663-11870596:+THYMEERENSG00000149021,SCGB1A10.25473.2731e-024.8509e-060.4475imageNNSCGB1A1
chr19:11869663-11870596:+THYMEERENSG00000084636,COL16A10.28143.8160e-022.4373e-050.4165imageNNCOL16A1Mast_cells_restingGSVA_HALLMARK_E2F_TARGETS
chr19:11869663-11870596:+THYMEERENSG00000204388,HSPA1B0.26994.8660e-023.0002e-050.4122imageNNHSPA1BB_cells_memoryGSVA_HALLMARK_SPERMATOGENESIS

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4. Enriched editing regions and immune related splicing for ZNF439


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
ENSG00000171291.7,ZNF439
THYMEAGA3ENSG00000146063.14chr5181234173:181234349:181234931:181234995:181234911:181234995-0.13303.4606e-021.5727e-05-0.4337imageNBUD13;CSTF2T;DGCR8;DKC1;EIF4A3;ELAVL1;FBL;FMR1;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;NONO;NOP58;PCBP2;PRPF8;SLTM;SRSF1;SRSF9;TAF15;TIA1;U2AF1;U2AF2;UPF1NAMacrophages_M1GSVA_HALLMARK_ALLOGRAFT_REJECTION
chr19:11869663-11870596:+
THYMEERMEXENSG00000143537.9chr1155061417:155061489:155061575:155061646:155061880:155061975:155062244:155062369-0.32791.2355e-023.9223e-04-0.4178imageNNADAM15Macrophages_M0GSVA_HALLMARK_ESTROGEN_RESPONSE_LATE
ENSG00000171291.7,ZNF439
THYMEAGIRENSG00000167615.12chr1954458313:54459352:54459464:54459481-0.32471.5574e-028.1594e-05-0.4096imageNBUD13;CSTF2T;DGCR8;DKC1;EIF4A3;ELAVL1;ELAVL3;FBL;FMR1;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;NONO;NOP58;PCBP2;PRPF8;SLTM;SRSF1;SRSF9;TAF15;TIA1;U2AF1;U2AF2;UPF1LENG8GSVA_HALLMARK_APICAL_JUNCTION
ENSG00000171291.7,ZNF439
THYMEAGMEXENSG00000143537.9chr1155061417:155061489:155061575:155061646:155061880:155061975:155062244:155062369-0.30732.6454e-026.7286e-04-0.4022imageNBUD13;CSTF2T;DGCR8;EIF4A3;ELAVL1;FBL;FMR1;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;NONO;NOP58;PCBP2;PRPF8;SLTM;SRSF1;SRSF9;TAF15;TIA1;U2AF1;U2AF2;UPF1ADAM15Macrophages_M0GSVA_HALLMARK_ESTROGEN_RESPONSE_LATE
ENSG00000171291.7,ZNF439
THYMEAGIRENSG00000144134.14chr2113637366:113641005:113641355:113641450-0.33031.6822e-022.6959e-05-0.4824imageNBUD13;CSTF2T;EIF4A3;ELAVL1;ELAVL3;FBL;FMR1;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPU;HNRNPUL1;IGF2BP2;NOP58;PCBP2;PRPF8;SLTM;SRSF1;SRSF9;TAF15;TIA1;U2AF1;U2AF2;UPF1NAT_cells_CD8GSVA_HALLMARK_PROTEIN_SECRETION
chr19:11869663-11870596:+
THYMEERIRENSG00000144134.14chr2113637366:113641005:113641355:113641450-0.32002.1937e-022.7763e-05-0.4818imageNNNAT_cells_CD8GSVA_HALLMARK_PROTEIN_SECRETION
chr19:11869663-11870596:+
THYMEERIRENSG00000167615.12chr1954458313:54459352:54459464:54459481-0.31242.1960e-028.3789e-05-0.4090imageNNLENG8GSVA_HALLMARK_APICAL_JUNCTION

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5. Enriched editing regions and immune infiltration for ZNF439


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
chr19:11869663-11870596:+BLCAEERB_cells_naive3.1891e-020.1862image
ENSG00000171291.7,ZNF439BRCAEAGMast_cells_resting4.8557e-02-0.1120image
ENSG00000171291.7,ZNF439ESCAEAGDendritic_cells_resting1.1783e-03-0.4337image
chr19:11869663-11870596:+KIRPEERPlasma_cells3.9179e-020.2956image
ENSG00000171291.7,ZNF439KIRPEAGPlasma_cells3.2246e-020.3003image
chr19:11852565-11853072:+LAMLEERMonocytes3.6019e-020.3609image
chr19:11869663-11870596:+LGGEERB_cells_memory4.1528e-02-0.1066image
ENSG00000171291.7,ZNF439LGGEAGB_cells_memory4.8865e-02-0.1029image
ENSG00000171291.7,ZNF439LUADEAGB_cells_memory6.0918e-030.5140image
chr19:11864379-11865956:+OVEEREosinophils2.1845e-050.5667image
chr19:11869663-11870596:+OVEERMast_cells_activated3.5242e-020.1834image
ENSG00000171291.7,ZNF439OVEAGMast_cells_activated5.1121e-040.2794image
chr19:11869663-11870596:+PCPGEERB_cells_naive8.9055e-030.3593image
ENSG00000171291.7,ZNF439PCPGEAGB_cells_naive8.5817e-030.3609image
ENSG00000171291.7,ZNF439SKCMEAGDendritic_cells_resting1.3040e-020.2699image
chr19:11864379-11865956:+STADEERT_cells_CD4_memory_activated1.9699e-030.4986image
ENSG00000171291.7,ZNF439STADEAGT_cells_regulatory_(Tregs)1.3527e-03-0.3177image
chr19:11869663-11870596:+UCECEERB_cells_memory9.2921e-030.3305image
ENSG00000171291.7,ZNF439UCECEAGB_cells_memory6.5155e-030.3317image


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6. Enriched editing regions and immune gene sets for ZNF439


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
ENSG00000171291.7,ZNF439STADEAG1.0786e-050.42643.8591e-040.34984.1343e-050.39981.0295e-040.3804image


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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
ENSG00000171291.7,ZNF439BLCAGSVA_HALLMARK_HYPOXIAEAG6.5677e-050.3308image
chr19:11869663-11870596:+BLCAGSVA_HALLMARK_IL2_STAT5_SIGNALINGEER5.0817e-040.2974image
ENSG00000171291.7,ZNF439BRCAGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG9.8439e-030.1462image
ENSG00000171291.7,ZNF439ESCAGSVA_HALLMARK_ANDROGEN_RESPONSEEAG2.0495e-030.4142image
ENSG00000171291.7,ZNF439KICHGSVA_HALLMARK_MYC_TARGETS_V2EAG3.3797e-020.3207image
ENSG00000171291.7,ZNF439KIRCGSVA_HALLMARK_BILE_ACID_METABOLISMEAG2.8955e-030.3722image
chr19:11869663-11870596:+KIRCGSVA_HALLMARK_GLYCOLYSISEER6.8227e-030.3640image
chr19:11852565-11853072:+LAMLGSVA_HALLMARK_HEME_METABOLISMEER4.7067e-02-0.3430image
chr19:11864379-11865956:+LAMLGSVA_HALLMARK_COAGULATIONEER2.3970e-020.2235image
ENSG00000171291.7,ZNF439LAMLGSVA_HALLMARK_COAGULATIONEAG1.9489e-020.2063image
ENSG00000171291.7,ZNF439LGGGSVA_HALLMARK_BILE_ACID_METABOLISMEAG3.1782e-050.2154image
chr19:11869663-11870596:+LGGGSVA_HALLMARK_BILE_ACID_METABOLISMEER2.7250e-050.2174image
ENSG00000171291.7,ZNF439LUADGSVA_HALLMARK_APICAL_JUNCTIONEAG3.3130e-020.4111image
ENSG00000171291.7,ZNF439OVGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEAG1.0493e-030.2641image
chr19:11864379-11865956:+OVGSVA_HALLMARK_PEROXISOMEEER4.7046e-030.3973image
chr19:11869663-11870596:+OVGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEER2.9609e-020.1894image
chr19:11869663-11870596:+SARCGSVA_HALLMARK_MYOGENESISEER2.9637e-020.2962image
ENSG00000171291.7,ZNF439SARCGSVA_HALLMARK_MYOGENESISEAG2.6496e-020.2965image
ENSG00000171291.7,ZNF439STADGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG4.3981e-090.5478image
chr19:11864379-11865956:+STADGSVA_HALLMARK_MTORC1_SIGNALINGEER1.2287e-030.5175image
chr19:11869663-11870596:+UCECGSVA_HALLMARK_ANDROGEN_RESPONSEEER5.4150e-040.4301image
ENSG00000171291.7,ZNF439UCECGSVA_HALLMARK_ANDROGEN_RESPONSEEAG2.8925e-040.4323image


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7. Enriched editing regions and drugs for ZNF439


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
chr19:11869663-11870596:+BLCACGP.60474EER1.0296e-03-0.2815image
ENSG00000171291.7,ZNF439BLCACGP.60474EAG4.3007e-03-0.2399image
ENSG00000171291.7,ZNF439BRCAGSK269962AEAG6.9517e-04-0.1916image
chr19:11869663-11870596:+BRCAGSK269962AEER2.4712e-03-0.1750image
ENSG00000171291.7,ZNF439ESCACCT007093EAG2.0202e-060.6003image
chr19:11869663-11870596:+GBMFTI.277EER7.5674e-03-0.2341image
ENSG00000171291.7,ZNF439GBMFTI.277EAG6.3379e-03-0.2392image
ENSG00000171291.7,ZNF439KICHCGP.082996EAG3.9264e-02-0.3119image
chr19:11869663-11870596:+KIRCCCT018159EER2.7836e-020.2994image
ENSG00000171291.7,ZNF439KIRPLapatinibEAG3.4207e-02-0.2972image
chr19:11869663-11870596:+KIRPLapatinibEER2.2026e-02-0.3265image
chr19:11852565-11853072:+LAMLImatinibEER2.6553e-020.3802image
chr19:11864379-11865956:+LAMLA.770041EER2.0659e-02-0.2289image
ENSG00000171291.7,ZNF439LAMLA.770041EAG5.5464e-03-0.2438image
ENSG00000171291.7,ZNF439LGGCCT018159EAG1.2866e-030.1674image
chr19:11869663-11870596:+LGGBIRB.0796EER8.6211e-040.1734image
ENSG00000171291.7,ZNF439LUADEmbelinEAG4.2423e-02-0.3933image
chr19:11869663-11870596:+OVCisplatinEER6.6875e-030.2350image
chr19:11864379-11865956:+OVJNK.9LEER4.5974e-030.3982image
ENSG00000171291.7,ZNF439OVCisplatinEAG2.9494e-040.2906image
chr19:11869663-11870596:+PCPGDocetaxelEER1.3452e-020.3407image
ENSG00000171291.7,ZNF439PCPGDocetaxelEAG1.3011e-020.3422image
ENSG00000171291.7,ZNF439PRADABT.888EAG1.1589e-020.2742image
ENSG00000171291.7,ZNF439SARCBicalutamideEAG4.1961e-02-0.2728image
ENSG00000171291.7,ZNF439SKCMAKT.inhibitor.VIIIEAG5.6047e-03-0.2997image
chr19:11864379-11865956:+STADABT.263EER3.6959e-030.4715image
ENSG00000171291.7,ZNF439STADCCT007093EAG8.1070e-040.3312image
ENSG00000171291.7,ZNF439THCABI.D1870EAG1.2373e-030.1784image
chr19:11869663-11870596:+THCABI.D1870EER1.5727e-030.1749image
ENSG00000171291.7,ZNF439THYMAUY922EAG2.6180e-030.3038image
chr19:11869663-11870596:+THYMAUY922EER5.4836e-030.2814image
chr19:11869663-11870596:+UCECAMG.706EER1.5146e-020.3097image
ENSG00000171291.7,ZNF439UCECMetforminEAG8.6806e-03-0.3206image


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