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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: TRAPPC3 (ImmuneEditome ID:27095)

1. Gene summary of enriched editing regions for TRAPPC3

check button Gene summary
Gene informationGene symbol

TRAPPC3

Gene ID

27095

GeneSynonymsBET3
GeneCytomap

1p34.3

GeneTypeprotein-coding
GeneDescriptiontrafficking protein particle complex subunit 3|trafficking protein particle complex 3
GeneModificationdate20230329
UniprotIDO43617;A6NKE1;A0A087WWM0;A0A087WYS5
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr1:36138737-36139478:-ENST00000497251.1ENSG00000054116.10TRAPPC3ncRNA_exonicAluSg7,AluSp,MIRchr1:36138737-36139478:-.alignment
chr1:36144437-36145350:-ENST00000469757.1ENSG00000054116.10TRAPPC3ncRNA_intronicMIRc,AluJb,AluYchr1:36144437-36145350:-.alignment
chr1:36144437-36145350:-ENST00000497251.1ENSG00000054116.10TRAPPC3ncRNA_intronicMIRc,AluJb,AluYchr1:36144437-36145350:-.alignment


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2. Tumor-specific enriched editing regions for TRAPPC3


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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 TRAPPC3


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 TRAPPC3


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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 TRAPPC3


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
chr1:36138737-36139478:-BLCAEERDendritic_cells_resting1.1834e-020.3313image
ENSG00000054116.10,TRAPPC3BLCAEAGDendritic_cells_resting1.1116e-020.3311image
chr1:36138737-36139478:-BRCAEERNK_cells_activated3.0770e-02-0.1330image
ENSG00000054116.10,TRAPPC3BRCAEAGB_cells_naive2.5329e-02-0.1369image
chr1:36138737-36139478:-CESCEERB_cells_memory4.6604e-020.3088image
ENSG00000054116.10,TRAPPC3CESCEAGB_cells_memory4.6604e-020.3088image
ENSG00000054116.10,TRAPPC3ESCAEAGMast_cells_activated6.2530e-030.4060image
chr1:36138737-36139478:-GBMEERB_cells_naive4.1996e-03-0.2505image
ENSG00000054116.10,TRAPPC3GBMEAGB_cells_naive4.1996e-03-0.2505image
ENSG00000054116.10,TRAPPC3HNSCEAGB_cells_memory4.1012e-020.4200image
chr1:36138737-36139478:-KIRCEERT_cells_gamma_delta3.2639e-020.3619image
ENSG00000054116.10,TRAPPC3KIRCEAGT_cells_gamma_delta3.2639e-020.3619image
chr1:36138737-36139478:-LUADEERT_cells_gamma_delta3.4407e-020.2128image
ENSG00000054116.10,TRAPPC3LUADEAGT_cells_gamma_delta3.4407e-020.2128image
chr1:36138737-36139478:-LUSCEERT_cells_gamma_delta3.6858e-020.2180image
ENSG00000054116.10,TRAPPC3LUSCEAGT_cells_gamma_delta3.6910e-020.2179image
chr1:36138737-36139478:-OVEERB_cells_memory2.8243e-030.2834image
ENSG00000054116.10,TRAPPC3OVEAGB_cells_memory2.1948e-030.2758image
ENSG00000054116.10,TRAPPC3PAADEAGT_cells_CD4_memory_activated2.0931e-020.5002image
chr1:36138737-36139478:-SARCEERT_cells_gamma_delta2.7739e-02-0.3319image
ENSG00000054116.10,TRAPPC3SARCEAGT_cells_gamma_delta2.7739e-02-0.3319image
ENSG00000054116.10,TRAPPC3STADEAGPlasma_cells1.8934e-020.2723image
chr1:36138737-36139478:-THCAEERMast_cells_activated2.7301e-020.1111image
ENSG00000054116.10,TRAPPC3THCAEAGMast_cells_activated2.7301e-020.1111image
ENSG00000054116.10,TRAPPC3THYMEAGNeutrophils1.1703e-030.6458image


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6. Enriched editing regions and immune gene sets for TRAPPC3


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
ENSG00000054116.10,TRAPPC3BLCAGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG4.9939e-020.2587image
ENSG00000054116.10,TRAPPC3BRCAGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG4.9356e-040.2118image
chr1:36138737-36139478:-BRCAGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEER1.9598e-030.1897image
chr1:36138737-36139478:-CESCGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEER1.1024e-02-0.3884image
ENSG00000054116.10,TRAPPC3CESCGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG1.1024e-02-0.3884image
ENSG00000054116.10,TRAPPC3GBMGSVA_HALLMARK_HEME_METABOLISMEAG8.6738e-040.2897image
chr1:36138737-36139478:-GBMGSVA_HALLMARK_HEME_METABOLISMEER8.6738e-040.2897image
ENSG00000054116.10,TRAPPC3HNSCGSVA_HALLMARK_KRAS_SIGNALING_UPEAG4.3568e-020.4153image
ENSG00000054116.10,TRAPPC3KIRCGSVA_HALLMARK_KRAS_SIGNALING_DNEAG3.6348e-020.3551image
chr1:36138737-36139478:-KIRCGSVA_HALLMARK_KRAS_SIGNALING_DNEER3.6348e-020.3551image
ENSG00000054116.10,TRAPPC3KIRPGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEAG2.0194e-02-0.4616image
chr1:36138737-36139478:-LGGGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEER2.2929e-020.1700image
ENSG00000054116.10,TRAPPC3LGGGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEAG2.2929e-020.1700image
chr1:36138737-36139478:-LUSCGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER1.3126e-020.2577image
ENSG00000054116.10,TRAPPC3LUSCGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG1.3183e-020.2576image
chr1:36138737-36139478:-OVGSVA_HALLMARK_MYC_TARGETS_V2EER4.2696e-020.1945image
ENSG00000054116.10,TRAPPC3OVGSVA_HALLMARK_MYC_TARGETS_V2EAG2.2545e-020.2073image
ENSG00000054116.10,TRAPPC3PAADGSVA_HALLMARK_MYC_TARGETS_V2EAG6.1438e-030.5773image
ENSG00000054116.10,TRAPPC3PRADGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEAG3.4770e-020.1890image
chr1:36138737-36139478:-PRADGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEER3.4770e-020.1890image
chr1:36138737-36139478:-SARCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEER9.7835e-030.3854image
ENSG00000054116.10,TRAPPC3SARCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG9.7835e-030.3854image
ENSG00000054116.10,TRAPPC3SKCMGSVA_HALLMARK_COAGULATIONEAG6.2955e-030.2290image
ENSG00000054116.10,TRAPPC3STADGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG1.4070e-020.2844image
ENSG00000054116.10,TRAPPC3THYMGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEAG4.7115e-03-0.5794image


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7. Enriched editing regions and drugs for TRAPPC3


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
ENSG00000054116.10,TRAPPC3BLCAABT.263EAG4.8834e-02-0.2599image
chr1:36138737-36139478:-BLCAABT.263EER4.4364e-02-0.2674image
ENSG00000054116.10,TRAPPC3BRCACisplatinEAG1.1572e-03-0.1978image
chr1:36138737-36139478:-BRCACisplatinEER7.8865e-04-0.2054image
chr1:36138737-36139478:-CESCKIN001.135EER6.5506e-030.4131image
ENSG00000054116.10,TRAPPC3CESCKIN001.135EAG6.5506e-030.4131image
ENSG00000054116.10,TRAPPC3ESCACisplatinEAG3.6132e-02-0.3168image
ENSG00000054116.10,TRAPPC3GBMLapatinibEAG1.0320e-03-0.2857image
chr1:36138737-36139478:-GBMLapatinibEER1.0320e-03-0.2857image
ENSG00000054116.10,TRAPPC3HNSCABT.888EAG2.3299e-02-0.4612image
ENSG00000054116.10,TRAPPC3KIRCCHIR.99021EAG1.3034e-020.4156image
chr1:36138737-36139478:-KIRCCHIR.99021EER1.3034e-020.4156image
ENSG00000054116.10,TRAPPC3KIRPBMS.754807EAG3.3549e-020.4264image
chr1:36138737-36139478:-LGGAZD6482EER3.9071e-020.1544image
ENSG00000054116.10,TRAPPC3LGGAZD6482EAG3.9071e-020.1544image
chr1:36138737-36139478:-LUADGNF.2EER3.8597e-02-0.2083image
ENSG00000054116.10,TRAPPC3LUADGNF.2EAG3.8597e-02-0.2083image
chr1:36138737-36139478:-LUSCLapatinibEER1.1600e-02-0.2635image
ENSG00000054116.10,TRAPPC3LUSCLapatinibEAG1.1583e-02-0.2636image
chr1:36138737-36139478:-OVGemcitabineEER8.4142e-03-0.2512image
ENSG00000054116.10,TRAPPC3OVAKT.inhibitor.VIIIEAG3.3966e-030.2643image
ENSG00000054116.10,TRAPPC3PAADFH535EAG4.7740e-020.4368image
ENSG00000054116.10,TRAPPC3PCPGAG.014699EAG4.9857e-020.3046image
ENSG00000054116.10,TRAPPC3PRADGefitinibEAG5.3747e-050.3531image
chr1:36138737-36139478:-PRADGefitinibEER5.3747e-050.3531image
chr1:36138737-36139478:-SARCGefitinibEER4.1989e-030.4233image
ENSG00000054116.10,TRAPPC3SARCGefitinibEAG4.1989e-030.4233image
ENSG00000054116.10,TRAPPC3SKCMCEP.701EAG2.0970e-02-0.1943image
ENSG00000054116.10,TRAPPC3STADMetforminEAG1.3179e-02-0.2870image
ENSG00000054116.10,TRAPPC3THYMEHT.1864EAG1.2342e-02-0.5238image


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