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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: NSUN4 (ImmuneEditome ID:387338)

1. Gene summary of enriched editing regions for NSUN4

check button Gene summary
Gene informationGene symbol

NSUN4

Gene ID

387338

GeneSynonymsSHTAP
GeneCytomap

1p33

GeneTypeprotein-coding
GeneDescription5-methylcytosine rRNA methyltransferase NSUN4|5-methylcytosine tRNA methyltransferase NSUN4|NOL1/NOP2/Sun domain family member 4|NOP2/Sun RNA methyltransferase family member 4|NOP2/Sun domain family, member 4|putative methyltransferase NSUN4|sperm head and tail associated protein
GeneModificationdate20230329
UniprotIDQ96CB9;Q6ZRQ1;M0R1K5;A0A087WUV3;A0A087X0V6
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr1:46347213-46348713:+ENST00000307089.6ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46347213-46348713:+ENST00000469918.4ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46347213-46348713:+ENST00000474844.4ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46347213-46348713:+ENST00000486270.4ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46347213-46348713:+ENST00000495427.1ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46347213-46348713:+ENST00000498008.4ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46347213-46348713:+ENST00000537428.2ENSG00000117481.9NSUN4intronicAluY,L2c,AluSx,AluSq2chr1:46347213-46348713:+.alignment
chr1:46352017-46352378:+ENST00000307089.6ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46352017-46352378:+ENST00000469918.4ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46352017-46352378:+ENST00000474844.4ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46352017-46352378:+ENST00000486270.4ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46352017-46352378:+ENST00000495427.1ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46352017-46352378:+ENST00000498008.4ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46352017-46352378:+ENST00000537428.2ENSG00000117481.9NSUN4intronicAluSx,FLAM_Cchr1:46352017-46352378:+.alignment
chr1:46356149-46358017:+ENST00000307089.6ENSG00000117481.9NSUN4intronicAluSx1,MamRep1894,L1MC4,AluYe5,L2,AluJbchr1:46356149-46358017:+.alignment
chr1:46356149-46358017:+ENST00000474844.4ENSG00000117481.9NSUN4intronicAluSx1,MamRep1894,L1MC4,AluYe5,L2,AluJbchr1:46356149-46358017:+.alignment
chr1:46356149-46358017:+ENST00000486270.4ENSG00000117481.9NSUN4intronicAluSx1,MamRep1894,L1MC4,AluYe5,L2,AluJbchr1:46356149-46358017:+.alignment
chr1:46356149-46358017:+ENST00000495427.1ENSG00000117481.9NSUN4intronicAluSx1,MamRep1894,L1MC4,AluYe5,L2,AluJbchr1:46356149-46358017:+.alignment
chr1:46356149-46358017:+ENST00000498008.4ENSG00000117481.9NSUN4intronicAluSx1,MamRep1894,L1MC4,AluYe5,L2,AluJbchr1:46356149-46358017:+.alignment
chr1:46356149-46358017:+ENST00000537428.2ENSG00000117481.9NSUN4intronicAluSx1,MamRep1894,L1MC4,AluYe5,L2,AluJbchr1:46356149-46358017:+.alignment
chr1:46363991-46364670:+ENST00000307089.6ENSG00000117481.9NSUN4UTR3L1ME1,AluSx1,AluJo,LTR108a_Mamchr1:46363991-46364670:+.alignment


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2. Tumor-specific enriched editing regions for NSUN4


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
ENSG00000117481.9,NSUN4PAADPathEAG3.9538e-021.7896e-02-0.4097image


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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 NSUN4


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

More results



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4. Enriched editing regions and immune related splicing for NSUN4


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

More results



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5. Enriched editing regions and immune infiltration for NSUN4


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
ENSG00000117481.9,NSUN4BLCAEAGT_cells_CD4_naive2.7746e-030.4144image
ENSG00000117481.9,NSUN4BRCAEAGNK_cells_activated3.8452e-020.1351image
ENSG00000117481.9,NSUN4COADEAGDendritic_cells_activated3.7575e-060.8272image
chr1:46347213-46348713:+ESCAEERT_cells_CD4_memory_resting3.7247e-020.3698image
ENSG00000117481.9,NSUN4ESCAEAGEosinophils1.6568e-020.2608image
ENSG00000117481.9,NSUN4GBMEAGMacrophages_M23.6278e-02-0.3166image
ENSG00000117481.9,NSUN4HNSCEAGDendritic_cells_resting2.5306e-020.3370image
chr1:46363991-46364670:+KIRCEERDendritic_cells_activated2.7084e-020.2127image
ENSG00000117481.9,NSUN4KIRCEAGDendritic_cells_activated2.7084e-020.2127image
ENSG00000117481.9,NSUN4KIRPEAGB_cells_naive1.1549e-030.5266image
ENSG00000117481.9,NSUN4LAMLEAGB_cells_naive4.6779e-020.2744image
ENSG00000117481.9,NSUN4LIHCEAGT_cells_regulatory_(Tregs)3.1820e-030.3632image
ENSG00000117481.9,NSUN4LUADEAGT_cells_gamma_delta3.3357e-070.5953image
ENSG00000117481.9,NSUN4LUSCEAGPlasma_cells3.5419e-020.2721image
chr1:46363991-46364670:+OVEERB_cells_naive1.0390e-02-0.2604image
ENSG00000117481.9,NSUN4OVEAGDendritic_cells_resting2.3205e-02-0.2098image
ENSG00000117481.9,NSUN4PCPGEAGPlasma_cells7.1825e-060.6381image
ENSG00000117481.9,NSUN4PRADEAGNK_cells_activated2.1593e-020.2262image
ENSG00000117481.9,NSUN4SARCEAGT_cells_CD4_memory_resting6.4565e-03-0.3249image
ENSG00000117481.9,NSUN4SKCMEAGNK_cells_activated1.1140e-030.3954image
chr1:46347213-46348713:+STADEERDendritic_cells_resting5.3940e-030.3770image
chr1:46352017-46352378:+STADEERT_cells_CD4_memory_activated2.0346e-020.4704image
chr1:46363991-46364670:+STADEERT_cells_gamma_delta3.1181e-060.3690image
ENSG00000117481.9,NSUN4STADEAGNK_cells_resting4.4558e-02-0.1467image
ENSG00000117481.9,NSUN4THCAEAGMacrophages_M03.6430e-020.2803image


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6. Enriched editing regions and immune gene sets for NSUN4


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
ENSG00000117481.9,NSUN4BLCAGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG2.1254e-03-0.4245image
ENSG00000117481.9,NSUN4BRCAGSVA_HALLMARK_MITOTIC_SPINDLEEAG7.8138e-03-0.1731image
ENSG00000117481.9,NSUN4COADGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEAG2.7471e-04-0.7144image
chr1:46347213-46348713:+ESCAGSVA_HALLMARK_PROTEIN_SECRETIONEER3.0516e-020.3830image
ENSG00000117481.9,NSUN4GBMGSVA_HALLMARK_HEDGEHOG_SIGNALINGEAG3.9387e-020.3118image
ENSG00000117481.9,NSUN4HNSCGSVA_HALLMARK_E2F_TARGETSEAG4.7534e-02-0.3004image
ENSG00000117481.9,NSUN4KIRPGSVA_HALLMARK_MITOTIC_SPINDLEEAG3.2674e-03-0.4833image
ENSG00000117481.9,NSUN4LAMLGSVA_HALLMARK_KRAS_SIGNALING_DNEAG2.3180e-020.3115image
ENSG00000117481.9,NSUN4LIHCGSVA_HALLMARK_MYOGENESISEAG5.2498e-040.4214image
ENSG00000117481.9,NSUN4LUADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG3.6809e-03-0.3635image
ENSG00000117481.9,NSUN4LUSCGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG4.2853e-02-0.2624image
ENSG00000117481.9,NSUN4OVGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG7.3604e-05-0.3581image
ENSG00000117481.9,NSUN4PRADGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEAG8.8966e-05-0.3764image
ENSG00000117481.9,NSUN4SARCGSVA_HALLMARK_MITOTIC_SPINDLEEAG8.6785e-03-0.3137image
ENSG00000117481.9,NSUN4SKCMGSVA_HALLMARK_KRAS_SIGNALING_DNEAG4.4137e-040.4234image
chr1:46352017-46352378:+STADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER1.7774e-020.4794image
chr1:46347213-46348713:+STADGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEER1.0768e-020.3476image
ENSG00000117481.9,NSUN4STADGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG1.0128e-04-0.2797image
chr1:46356149-46358017:+STADGSVA_HALLMARK_KRAS_SIGNALING_DNEER6.7343e-030.4072image
ENSG00000117481.9,NSUN4THCAGSVA_HALLMARK_UV_RESPONSE_DNEAG3.8385e-02-0.2775image
ENSG00000117481.9,NSUN4UCECGSVA_HALLMARK_ADIPOGENESISEAG8.2853e-03-0.5729image


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7. Enriched editing regions and drugs for NSUN4


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
ENSG00000117481.9,NSUN4BLCABexaroteneEAG1.0730e-020.3578image
ENSG00000117481.9,NSUN4BRCAGefitinibEAG4.9870e-02-0.1289image
ENSG00000117481.9,NSUN4COADAZ628EAG1.6492e-040.7314image
chr1:46347213-46348713:+ESCAAMG.706EER5.4619e-030.4797image
ENSG00000117481.9,NSUN4ESCAJW.7.52.1EAG1.2819e-020.2705image
ENSG00000117481.9,NSUN4GBMEtoposideEAG9.5288e-030.3866image
ENSG00000117481.9,NSUN4HNSCGemcitabineEAG2.2957e-020.3423image
ENSG00000117481.9,NSUN4KIRCJNK.9LEAG2.3561e-050.3948image
chr1:46363991-46364670:+KIRCJNK.9LEER2.3561e-050.3948image
ENSG00000117481.9,NSUN4KIRPAZD8055EAG2.8457e-02-0.3705image
ENSG00000117481.9,NSUN4LGGGDC0941EAG2.3612e-03-0.2577image
ENSG00000117481.9,NSUN4LIHCCEP.701EAG2.1262e-04-0.4471image
ENSG00000117481.9,NSUN4LUADABT.263EAG1.7185e-02-0.3017image
chr1:46363991-46364670:+OVA.770041EER3.7996e-04-0.3554image
ENSG00000117481.9,NSUN4OVAG.014699EAG1.9962e-03-0.2829image
ENSG00000117481.9,NSUN4PCPGBortezomibEAG1.3608e-02-0.3824image
ENSG00000117481.9,NSUN4PRADAG.014699EAG1.0663e-04-0.3725image
ENSG00000117481.9,NSUN4SARCAZD.2281EAG1.9238e-05-0.4900image
ENSG00000117481.9,NSUN4SKCMErlotinibEAG4.2441e-06-0.5358image
chr1:46352017-46352378:+STADBicalutamideEER3.7128e-02-0.4276image
chr1:46347213-46348713:+STADAICAREER1.3076e-020.3388image
chr1:46363991-46364670:+STADA.770041EER1.8109e-02-0.1928image
chr1:46356149-46358017:+STADGDC0941EER1.6921e-02-0.3624image
ENSG00000117481.9,NSUN4THCAAKT.inhibitor.VIIIEAG3.0272e-030.3892image


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