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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: TMED4 (ImmuneEditome ID:222068)

1. Gene summary of enriched editing regions for TMED4

check button Gene summary
Gene informationGene symbol

TMED4

Gene ID

222068

GeneSynonymsERS25|GMP25iso|HNLF|p24a3|p24alpha3
GeneCytomap

7p13

GeneTypeprotein-coding
GeneDescriptiontransmembrane emp24 domain-containing protein 4|endoplasmic reticulum stress-response protein 25 kDa|p24 family protein alpha-3|putative NF-kappa-B-activating protein 156|putative NFkB activating protein HNLF|transmembrane emp24 protein transport domain containing 4
GeneModificationdate20230329
UniprotIDQ7Z7H5;F8W7F7
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr7:44580187-44580958:-ENST00000477639.4ENSG00000158604.13TMED4ncRNA_exonicAluSp,AluSx,L1MB3chr7:44580187-44580958:-.alignment


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2. Tumor-specific enriched editing regions for TMED4


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
chr7:44580187-44580958:-STADEER4.7152e-02image
ENSG00000158604.13,TMED4STADEAG4.7624e-02image


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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 TMED4


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
chr7:44580187-44580958:-LAMLEERENSG00000167272,POP5-0.46846.5859e-033.5667e-06-0.4203imageNAUH;ELAVL1;FBL;GTF2F1;RBM10;SAFB2;SLTM;SRSF1;YTHDF1NAEosinophilsGSVA_HALLMARK_DNA_REPAIR

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4. Enriched editing regions and immune related splicing for TMED4


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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 TMED4


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
chr7:44580187-44580958:-ACCEERT_cells_follicular_helper3.3131e-02-0.3967image
ENSG00000158604.13,TMED4ACCEAGT_cells_follicular_helper3.3131e-02-0.3967image
chr7:44580187-44580958:-BLCAEERDendritic_cells_resting4.7586e-020.1885image
ENSG00000158604.13,TMED4BLCAEAGDendritic_cells_resting4.7586e-020.1885image
chr7:44580187-44580958:-BRCAEERT_cells_gamma_delta9.2376e-030.1266image
ENSG00000158604.13,TMED4BRCAEAGT_cells_gamma_delta8.6931e-030.1274image
chr7:44580187-44580958:-CESCEERB_cells_naive2.3512e-03-0.3855image
ENSG00000158604.13,TMED4CESCEAGB_cells_naive2.3512e-03-0.3855image
chr7:44580187-44580958:-COADEERNK_cells_activated2.5680e-030.3707image
ENSG00000158604.13,TMED4COADEAGNK_cells_activated1.5799e-030.3814image
chr7:44580187-44580958:-ESCAEERNK_cells_resting1.7538e-040.3186image
ENSG00000158604.13,TMED4ESCAEAGNK_cells_resting1.8628e-040.3174image
chr7:44580187-44580958:-GBMEERMacrophages_M21.6110e-04-0.3686image
ENSG00000158604.13,TMED4GBMEAGMacrophages_M21.1858e-04-0.3737image
chr7:44580187-44580958:-HNSCEERMast_cells_activated1.0795e-020.2854image
ENSG00000158604.13,TMED4HNSCEAGMast_cells_activated1.1651e-020.2808image
chr7:44580187-44580958:-KIRCEERDendritic_cells_activated3.3220e-080.4246image
ENSG00000158604.13,TMED4KIRCEAGDendritic_cells_activated3.3220e-080.4246image
chr7:44580187-44580958:-KIRPEERT_cells_CD4_memory_activated6.6740e-030.3788image
chr7:44580187-44580958:-LGGEERT_cells_CD4_memory_resting6.6007e-030.1802image
ENSG00000158604.13,TMED4LGGEAGT_cells_CD4_memory_resting6.6007e-030.1802image
chr7:44580187-44580958:-LUADEEREosinophils9.8486e-030.2035image
ENSG00000158604.13,TMED4LUADEAGEosinophils9.8486e-030.2035image
chr7:44580187-44580958:-LUSCEERNK_cells_activated1.0809e-020.2171image
ENSG00000158604.13,TMED4LUSCEAGNK_cells_activated1.0809e-020.2171image
ENSG00000158604.13,TMED4MESOEAGDendritic_cells_activated2.7314e-050.7256image
chr7:44580187-44580958:-OVEERMacrophages_M21.5089e-02-0.2709image
ENSG00000158604.13,TMED4OVEAGMacrophages_M21.5820e-02-0.2690image
ENSG00000158604.13,TMED4PAADEAGDendritic_cells_activated3.0938e-020.2659image
ENSG00000158604.13,TMED4PRADEAGT_cells_CD4_memory_resting2.9699e-030.3281image
ENSG00000158604.13,TMED4READEAGMast_cells_activated2.1183e-020.5114image
chr7:44580187-44580958:-SARCEERT_cells_CD4_memory_activated9.6162e-030.2716image
ENSG00000158604.13,TMED4SARCEAGT_cells_CD4_memory_activated9.6162e-030.2716image
chr7:44580187-44580958:-SKCMEERNeutrophils2.3966e-020.2152image
ENSG00000158604.13,TMED4SKCMEAGNeutrophils2.3008e-020.2157image
chr7:44580187-44580958:-STADEERT_cells_CD4_memory_activated1.0843e-030.1903image
ENSG00000158604.13,TMED4STADEAGT_cells_CD4_memory_activated1.4800e-030.1852image
chr7:44580187-44580958:-TGCTEERT_cells_follicular_helper2.4209e-020.3037image
ENSG00000158604.13,TMED4TGCTEAGT_cells_follicular_helper2.4209e-020.3037image
ENSG00000158604.13,TMED4THCAEAGEosinophils4.6161e-030.4614image
chr7:44580187-44580958:-UCECEERT_cells_regulatory_(Tregs)4.8164e-020.3364image
ENSG00000158604.13,TMED4UCECEAGT_cells_regulatory_(Tregs)4.8164e-020.3364image


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6. Enriched editing regions and immune gene sets for TMED4


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
chr7:44580187-44580958:-ACCGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEER1.4552e-02-0.4490image
ENSG00000158604.13,TMED4ACCGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEAG1.4552e-02-0.4490image
chr7:44580187-44580958:-BLCAGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER4.2776e-020.1927image
ENSG00000158604.13,TMED4BLCAGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG4.2776e-020.1927image
chr7:44580187-44580958:-BRCAGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER1.7427e-020.1157image
ENSG00000158604.13,TMED4BRCAGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG5.0610e-030.1361image
chr7:44580187-44580958:-CESCGSVA_HALLMARK_BILE_ACID_METABOLISMEER1.4651e-03-0.4017image
ENSG00000158604.13,TMED4CESCGSVA_HALLMARK_BILE_ACID_METABOLISMEAG1.4651e-03-0.4017image
chr7:44580187-44580958:-COADGSVA_HALLMARK_BILE_ACID_METABOLISMEER2.8519e-02-0.2739image
ENSG00000158604.13,TMED4ESCAGSVA_HALLMARK_P53_PATHWAYEAG1.8037e-020.2040image
chr7:44580187-44580958:-ESCAGSVA_HALLMARK_P53_PATHWAYEER2.0896e-020.1994image
chr7:44580187-44580958:-GBMGSVA_HALLMARK_HEME_METABOLISMEER9.4431e-03-0.2584image
ENSG00000158604.13,TMED4GBMGSVA_HALLMARK_HEME_METABOLISMEAG7.9002e-03-0.2629image
chr7:44580187-44580958:-HNSCGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER9.7307e-03-0.2892image
ENSG00000158604.13,TMED4HNSCGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG3.7928e-02-0.2325image
ENSG00000158604.13,TMED4KIRCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG1.6436e-02-0.1918image
chr7:44580187-44580958:-KIRCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEER1.6436e-02-0.1918image
ENSG00000158604.13,TMED4KIRPGSVA_HALLMARK_KRAS_SIGNALING_DNEAG2.4645e-020.3175image
chr7:44580187-44580958:-KIRPGSVA_HALLMARK_KRAS_SIGNALING_DNEER4.2491e-020.2881image
chr7:44580187-44580958:-LAMLGSVA_HALLMARK_BILE_ACID_METABOLISMEER8.2747e-03-0.2473image
ENSG00000158604.13,TMED4LAMLGSVA_HALLMARK_BILE_ACID_METABOLISMEAG2.3882e-02-0.2097image
ENSG00000158604.13,TMED4LGGGSVA_HALLMARK_BILE_ACID_METABOLISMEAG1.9831e-03-0.2047image
chr7:44580187-44580958:-LGGGSVA_HALLMARK_BILE_ACID_METABOLISMEER1.9831e-03-0.2047image
ENSG00000158604.13,TMED4LUADGSVA_HALLMARK_MYOGENESISEAG2.4124e-04-0.2864image
chr7:44580187-44580958:-LUADGSVA_HALLMARK_MYOGENESISEER2.4124e-04-0.2864image
ENSG00000158604.13,TMED4MESOGSVA_HALLMARK_GLYCOLYSISEAG4.8091e-02-0.3913image
chr7:44580187-44580958:-OVGSVA_HALLMARK_PROTEIN_SECRETIONEER4.1906e-03-0.3168image
ENSG00000158604.13,TMED4OVGSVA_HALLMARK_PROTEIN_SECRETIONEAG4.5797e-03-0.3139image
chr7:44580187-44580958:-PCPGGSVA_HALLMARK_HYPOXIAEER1.0031e-020.2686image
ENSG00000158604.13,TMED4PCPGGSVA_HALLMARK_HYPOXIAEAG1.0031e-020.2686image
ENSG00000158604.13,TMED4PRADGSVA_HALLMARK_UV_RESPONSE_UPEAG5.3736e-08-0.5632image
ENSG00000158604.13,TMED4READGSVA_HALLMARK_SPERMATOGENESISEAG1.5550e-020.5329image
chr7:44580187-44580958:-SARCGSVA_HALLMARK_COMPLEMENTEER1.9367e-020.2461image
ENSG00000158604.13,TMED4SARCGSVA_HALLMARK_COMPLEMENTEAG1.9367e-020.2461image
chr7:44580187-44580958:-SKCMGSVA_HALLMARK_PROTEIN_SECRETIONEER1.7348e-02-0.2265image
ENSG00000158604.13,TMED4SKCMGSVA_HALLMARK_PROTEIN_SECRETIONEAG1.4949e-02-0.2305image
chr7:44580187-44580958:-STADGSVA_HALLMARK_MYOGENESISEER1.9098e-02-0.1371image
ENSG00000158604.13,TMED4STADGSVA_HALLMARK_MYOGENESISEAG2.0967e-02-0.1351image
ENSG00000158604.13,TMED4TGCTGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG3.2307e-030.3902image
chr7:44580187-44580958:-TGCTGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER3.2307e-030.3902image
ENSG00000158604.13,TMED4UCECGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG8.9686e-04-0.5363image
chr7:44580187-44580958:-UCECGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER8.9686e-04-0.5363image


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7. Enriched editing regions and drugs for TMED4


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
chr7:44580187-44580958:-ACCATRAEER1.6940e-020.4399image
ENSG00000158604.13,TMED4ACCATRAEAG1.6940e-020.4399image
ENSG00000158604.13,TMED4BRCAKU.55933EAG3.3592e-03-0.1423image
chr7:44580187-44580958:-BRCACMKEER7.6459e-03-0.1298image
chr7:44580187-44580958:-CESCGW843682XEER3.6102e-04-0.4455image
ENSG00000158604.13,TMED4CESCGW843682XEAG3.6102e-04-0.4455image
chr7:44580187-44580958:-COADBMS.708163EER4.1249e-02-0.2559image
chr7:44580187-44580958:-ESCAGefitinibEER2.1998e-08-0.4618image
ENSG00000158604.13,TMED4ESCAGefitinibEAG2.5223e-08-0.4601image
chr7:44580187-44580958:-GBMAxitinibEER1.1299e-02-0.2524image
ENSG00000158604.13,TMED4GBMAxitinibEAG1.2716e-02-0.2471image
chr7:44580187-44580958:-HNSCAZD6244EER5.5928e-04-0.3796image
ENSG00000158604.13,TMED4HNSCAZD6244EAG5.5928e-04-0.3796image
ENSG00000158604.13,TMED4KIRCAZD6244EAG3.5797e-03-0.2319image
chr7:44580187-44580958:-KIRCAZD6244EER3.5797e-03-0.2319image
chr7:44580187-44580958:-KIRPBleomycinEER3.7973e-020.2944image
ENSG00000158604.13,TMED4KIRPBleomycinEAG2.3692e-020.3196image
chr7:44580187-44580958:-LAMLFTI.277EER9.8236e-03-0.2420image
ENSG00000158604.13,TMED4LAMLFTI.277EAG8.9277e-03-0.2418image
chr7:44580187-44580958:-LGGKIN001.135EER2.4542e-030.2005image
ENSG00000158604.13,TMED4LGGKIN001.135EAG2.4542e-030.2005image
ENSG00000158604.13,TMED4LIHCEtoposideEAG2.7146e-020.3409image
chr7:44580187-44580958:-LUADBexaroteneEER5.8893e-070.3827image
ENSG00000158604.13,TMED4LUADBexaroteneEAG5.8893e-070.3827image
ENSG00000158604.13,TMED4LUSCAZD6244EAG4.2467e-04-0.2970image
chr7:44580187-44580958:-LUSCAZD6244EER4.2467e-04-0.2970image
ENSG00000158604.13,TMED4MESOAUY922EAG1.2842e-050.7447image
chr7:44580187-44580958:-OVAS601245EER8.5457e-050.4249image
ENSG00000158604.13,TMED4OVAS601245EAG7.3314e-050.4285image
ENSG00000158604.13,TMED4PAADAMG.706EAG1.9399e-020.2872image
chr7:44580187-44580958:-PCPGAZD.2281EER2.3197e-05-0.4280image
ENSG00000158604.13,TMED4PCPGAZD.2281EAG2.3197e-05-0.4280image
ENSG00000158604.13,TMED4PRADLenalidomideEAG3.2584e-07-0.5346image
chr7:44580187-44580958:-SARCCCT007093EER2.2487e-030.3181image
ENSG00000158604.13,TMED4SARCCCT007093EAG2.2487e-030.3181image
ENSG00000158604.13,TMED4SKCMA.770041EAG2.2970e-03-0.2865image
chr7:44580187-44580958:-SKCMA.770041EER2.4742e-03-0.2858image
chr7:44580187-44580958:-STADImatinibEER3.7739e-040.2067image
ENSG00000158604.13,TMED4STADImatinibEAG4.4658e-040.2042image
ENSG00000158604.13,TMED4TGCTGefitinibEAG9.1619e-04-0.4346image
chr7:44580187-44580958:-TGCTGefitinibEER9.1619e-04-0.4346image
ENSG00000158604.13,TMED4THCAEmbelinEAG2.6466e-020.3697image
chr7:44580187-44580958:-UCECCI.1040EER3.8109e-03-0.4764image
ENSG00000158604.13,TMED4UCECCI.1040EAG3.8109e-03-0.4764image


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