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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: TRAF1 (ImmuneEditome ID:7185)

1. Gene summary of enriched editing regions for TRAF1

check button Gene summary
Gene informationGene symbol

TRAF1

Gene ID

7185

GeneSynonymsEBI6|MGC:10353
GeneCytomap

9q33.2

GeneTypeprotein-coding
GeneDescriptionTNF receptor-associated factor 1|Epstein-Bar virus-induced protein 6
GeneModificationdate20230517
UniprotIDQ13077
PubMed ID

32093731

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr9:120927351-120928230:-ENST00000373887.6ENSG00000056558.9TRAF1UTR5MIRb,MIRchr9:120927351-120928230:-.alignment


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2. Tumor-specific enriched editing regions for TRAF1


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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 TRAF1


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 TRAF1


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

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5. Enriched editing regions and immune infiltration for TRAF1


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
ENSG00000056558.9,TRAF1BLCAEAGNK_cells_activated4.0967e-02-0.3692image
chr9:120927351-120928230:-BRCAEERT_cells_CD4_memory_activated2.4017e-02-0.1442image
ENSG00000056558.9,TRAF1BRCAEAGT_cells_CD4_memory_activated2.4057e-02-0.1441image
ENSG00000056558.9,TRAF1CESCEAGMast_cells_resting1.2488e-02-0.4920image
ENSG00000056558.9,TRAF1COADEAGNeutrophils1.9625e-030.5423image
chr9:120927351-120928230:-ESCAEERB_cells_memory2.8372e-020.3102image
ENSG00000056558.9,TRAF1ESCAEAGB_cells_memory2.8372e-020.3102image
chr9:120927351-120928230:-KIRCEERMast_cells_resting1.1310e-020.2215image
ENSG00000056558.9,TRAF1KIRCEAGMast_cells_resting1.1310e-020.2215image
ENSG00000056558.9,TRAF1LAMLEAGPlasma_cells3.1148e-030.3882image
chr9:120927351-120928230:-LGGEERPlasma_cells2.0463e-060.5232image
ENSG00000056558.9,TRAF1LGGEAGPlasma_cells2.0463e-060.5232image
ENSG00000056558.9,TRAF1LUADEAGNeutrophils1.9434e-020.2017image
chr9:120927351-120928230:-LUSCEERDendritic_cells_activated1.1207e-02-0.2755image
ENSG00000056558.9,TRAF1LUSCEAGDendritic_cells_activated1.1207e-02-0.2755image
ENSG00000056558.9,TRAF1OVEAGMacrophages_M03.4007e-02-0.3204image
ENSG00000056558.9,TRAF1PAADEAGT_cells_gamma_delta6.4593e-030.4398image
chr9:120927351-120928230:-PCPGEERMonocytes4.8204e-020.3270image
ENSG00000056558.9,TRAF1PCPGEAGMonocytes4.8204e-020.3270image
chr9:120927351-120928230:-SKCMEERT_cells_CD4_memory_activated9.8731e-03-0.2387image
ENSG00000056558.9,TRAF1SKCMEAGT_cells_CD4_memory_activated1.1201e-02-0.2337image
chr9:120927351-120928230:-STADEERNK_cells_resting4.6685e-020.2670image
chr9:120927351-120928230:-THCAEERB_cells_naive3.6402e-020.2026image
ENSG00000056558.9,TRAF1THCAEAGB_cells_naive3.6402e-020.2026image
ENSG00000056558.9,TRAF1THYMEAGMast_cells_resting1.6646e-050.7282image


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6. Enriched editing regions and immune gene sets for TRAF1


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
ENSG00000056558.9,TRAF1BRCAEAG6.2302e-03-0.17432.3525e-04-0.23292.7298e-02-0.14101.6307e-020.1533image
chr9:120927351-120928230:-BRCAEER6.2635e-03-0.17422.3562e-04-0.23292.7404e-02-0.14091.6186e-020.1535image


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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
ENSG00000056558.9,TRAF1ACCGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEAG3.1206e-02-0.4316image
chr9:120927351-120928230:-ACCGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEER3.1206e-02-0.4316image
ENSG00000056558.9,TRAF1BLCAGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEAG1.1633e-050.7001image
ENSG00000056558.9,TRAF1BRCAGSVA_HALLMARK_E2F_TARGETSEAG7.0368e-05-0.2512image
chr9:120927351-120928230:-BRCAGSVA_HALLMARK_E2F_TARGETSEER7.0875e-05-0.2510image
ENSG00000056558.9,TRAF1CESCGSVA_HALLMARK_MYC_TARGETS_V2EAG1.3209e-020.4886image
ENSG00000056558.9,TRAF1ESCAGSVA_HALLMARK_SPERMATOGENESISEAG9.8916e-03-0.3615image
chr9:120927351-120928230:-ESCAGSVA_HALLMARK_SPERMATOGENESISEER9.8916e-03-0.3615image
chr9:120927351-120928230:-GBMGSVA_HALLMARK_APICAL_SURFACEEER1.5701e-02-0.5084image
ENSG00000056558.9,TRAF1GBMGSVA_HALLMARK_APICAL_SURFACEEAG1.5701e-02-0.5084image
chr9:120927351-120928230:-KIRCGSVA_HALLMARK_UV_RESPONSE_DNEER1.1331e-020.2215image
ENSG00000056558.9,TRAF1KIRCGSVA_HALLMARK_UV_RESPONSE_DNEAG1.1331e-020.2215image
chr9:120927351-120928230:-KIRPGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER2.0723e-02-0.2358image
ENSG00000056558.9,TRAF1KIRPGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG2.0723e-02-0.2358image
ENSG00000056558.9,TRAF1LAMLGSVA_HALLMARK_NOTCH_SIGNALINGEAG1.2453e-02-0.3319image
ENSG00000056558.9,TRAF1LUADGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEAG2.5867e-040.3107image
chr9:120927351-120928230:-LUSCGSVA_HALLMARK_NOTCH_SIGNALINGEER5.2310e-030.3021image
ENSG00000056558.9,TRAF1LUSCGSVA_HALLMARK_NOTCH_SIGNALINGEAG5.2310e-030.3021image
ENSG00000056558.9,TRAF1MESOGSVA_HALLMARK_DNA_REPAIREAG2.5900e-020.4967image
chr9:120927351-120928230:-SKCMGSVA_HALLMARK_HEDGEHOG_SIGNALINGEER4.6026e-020.1856image
ENSG00000056558.9,TRAF1SKCMGSVA_HALLMARK_HEDGEHOG_SIGNALINGEAG4.4081e-020.1865image
ENSG00000056558.9,TRAF1STADGSVA_HALLMARK_P53_PATHWAYEAG6.5287e-030.3594image
chr9:120927351-120928230:-STADGSVA_HALLMARK_HYPOXIAEER1.2812e-020.3306image
chr9:120927351-120928230:-THCAGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER4.2416e-030.2744image
ENSG00000056558.9,TRAF1THCAGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG4.2416e-030.2744image
ENSG00000056558.9,TRAF1THYMGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG3.4194e-02-0.4089image


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7. Enriched editing regions and drugs for TRAF1


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
ENSG00000056558.9,TRAF1ACCImatinibEAG1.2221e-02-0.4933image
chr9:120927351-120928230:-ACCImatinibEER1.2221e-02-0.4933image
ENSG00000056558.9,TRAF1BLCAEtoposideEAG8.3268e-040.5692image
chr9:120927351-120928230:-BRCABicalutamideEER3.7338e-06-0.2906image
ENSG00000056558.9,TRAF1BRCABicalutamideEAG3.7798e-06-0.2904image
ENSG00000056558.9,TRAF1CESCDoxorubicinEAG1.3108e-04-0.6910image
ENSG00000056558.9,TRAF1COADDMOGEAG1.6478e-02-0.4343image
ENSG00000056558.9,TRAF1ESCACI.1040EAG5.6007e-04-0.4708image
chr9:120927351-120928230:-ESCACI.1040EER5.6007e-04-0.4708image
chr9:120927351-120928230:-GBMBosutinibEER1.0275e-030.6512image
ENSG00000056558.9,TRAF1GBMBosutinibEAG1.0275e-030.6512image
chr9:120927351-120928230:-KIRCCGP.082996EER2.5701e-030.2623image
ENSG00000056558.9,TRAF1KIRCCGP.082996EAG2.5701e-030.2623image
chr9:120927351-120928230:-KIRPBortezomibEER2.1263e-020.2349image
ENSG00000056558.9,TRAF1KIRPBortezomibEAG2.1263e-020.2349image
ENSG00000056558.9,TRAF1LAMLCI.1040EAG9.3816e-030.3442image
ENSG00000056558.9,TRAF1LGGFH535EAG1.3582e-020.2877image
chr9:120927351-120928230:-LGGFH535EER1.3582e-020.2877image
ENSG00000056558.9,TRAF1LUADATRAEAG7.6879e-030.2293image
ENSG00000056558.9,TRAF1LUSCMidostaurinEAG1.7987e-02-0.2576image
chr9:120927351-120928230:-LUSCMidostaurinEER1.7987e-02-0.2576image
ENSG00000056558.9,TRAF1MESOKU.55933EAG1.1189e-030.6740image
ENSG00000056558.9,TRAF1OVCamptothecinEAG4.6735e-020.3015image
ENSG00000056558.9,TRAF1PAADGefitinibEAG2.9971e-040.5683image
ENSG00000056558.9,TRAF1PRADMethotrexateEAG4.7467e-02-0.3711image
ENSG00000056558.9,TRAF1SARCJNK.9LEAG2.2534e-03-0.4107image
ENSG00000056558.9,TRAF1SKCMBortezomibEAG6.6016e-040.3104image
chr9:120927351-120928230:-SKCMBortezomibEER7.2796e-040.3093image
ENSG00000056558.9,TRAF1STADBleomycinEAG4.3274e-02-0.2711image
chr9:120927351-120928230:-STADBleomycinEER3.8013e-02-0.2780image
chr9:120927351-120928230:-THCAAMG.706EER4.0758e-020.1982image
ENSG00000056558.9,TRAF1THCAAMG.706EAG4.0758e-020.1982image
ENSG00000056558.9,TRAF1THYMBicalutamideEAG1.5226e-02-0.4621image


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