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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: RPL34 (ImmuneEditome ID:6164)

1. Gene summary of enriched editing regions for RPL34

check button Gene summary
Gene informationGene symbol

RPL34

Gene ID

6164

GeneSynonymsL34|eL34
GeneCytomap

4q25

GeneTypeprotein-coding
GeneDescription60S ribosomal protein L34|large ribosomal subunit protein eL34|leukemia-associated protein
GeneModificationdate20230329
UniprotIDP49207;A1LUY1
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr4:108623035-108623665:+ENST00000503574.1ENSG00000109475.15RPL34ncRNA_exonicAluSc8,AluSpchr4:108623035-108623665:+.alignment
chr4:108625466-108629008:+ENST00000502534.4ENSG00000109475.15RPL34UTR3AluSc8,AluSx1,AluSp,MIR,AluSx,AluJr,AluJbchr4:108625466-108629008:+.alignment


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2. Tumor-specific enriched editing regions for RPL34


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
ENSG00000109475.15,RPL34THCAEAG3.6030e-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 RPL34


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
chr4:108623035-108623665:+ESCAEERENSG00000167702,KIFC20.38737.7950e-033.9935e-090.5186imageNIGF2BP2;NOP56;U2AF2NAMacrophages_M0GSVA_HALLMARK_HYPOXIA
chr4:108623035-108623665:+ESCAEERENSG00000178896,EXOSC40.36011.5204e-021.0581e-050.4013imageNIGF2BP2;NOP56;U2AF2NAMast_cells_activatedGSVA_HALLMARK_MYC_TARGETS_V2

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4. Enriched editing regions and immune related splicing for RPL34


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
ENSG00000109475.15,RPL34
ESCAEAGA3ENSG00000165416.10chr1352659178:52659249:52661477:52661570:52661474:526615700.39661.3317e-029.7397e-070.4296imageNACIN1;AUH;BCCIP;BUD13;CELF2;CPSF6;CSTF2T;DDX3X;DDX42;DDX54;DGCR8;DHX9;DKC1;EIF4A3;EIF4G2;ELAVL1;ELAVL3;EWSR1;FAM120A;FBL;FMR1;FUS;FXR1;FXR2;GNL3;GTF2F1;HNRNPA1;HNRNPC;HNRNPK;HNRNPL;HNRNPM;IGF2BP1;IGF2BP2;IGF2BP3;ILF3;KHDRBS2;KHDRBS3;KHSRP;LARP4B;LIN28;LIN28A;LIN28B;MBNL2;MOV10;MSI2;NONO;NOP56;NOP58;NUMA1;PRPF8;PTBP1;QKI;RANGAP1;RBFOX2;RBM10;RBM22;RBM47;RBM5;RC3H1;RNF219;RTCB;SF3A3;SF3B4;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARDBP;TIA1;TIAL1;TNRC6A;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;XRN2;YTHDC1;YWHAG;ZC3H7B;ZNF184SUGT1Macrophages_M0GSVA_HALLMARK_P53_PATHWAY
chr4:108623035-108623665:+
ESCAEERA3ENSG00000165416.10chr1352659178:52659249:52661477:52661570:52661474:526615700.40571.2702e-021.9416e-060.4305imageNIGF2BP2;NOP56;U2AF2SUGT1Macrophages_M0GSVA_HALLMARK_P53_PATHWAY

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5. Enriched editing regions and immune infiltration for RPL34


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
chr4:108623035-108623665:+BLCAEERPlasma_cells1.1881e-030.4087image
ENSG00000109475.15,RPL34BLCAEAGPlasma_cells1.0449e-030.4096image
chr4:108625466-108629008:+BRCAEERNK_cells_activated6.0154e-030.3207image
ENSG00000109475.15,RPL34BRCAEAGNK_cells_activated2.4474e-030.2180image
chr4:108623035-108623665:+COADEERNeutrophils6.6028e-030.4387image
ENSG00000109475.15,RPL34COADEAGNeutrophils6.6028e-030.4387image
chr4:108623035-108623665:+ESCAEERT_cells_regulatory_(Tregs)1.6175e-02-0.2258image
ENSG00000109475.15,RPL34ESCAEAGB_cells_naive1.2989e-02-0.2262image
ENSG00000109475.15,RPL34HNSCEAGMonocytes2.8815e-020.4660image
chr4:108623035-108623665:+KIRCEERDendritic_cells_resting2.8224e-02-0.4388image
ENSG00000109475.15,RPL34KIRCEAGDendritic_cells_resting1.6616e-02-0.3913image
ENSG00000109475.15,RPL34LAMLEAGMacrophages_M17.1508e-030.2817image
chr4:108625466-108629008:+LGGEERB_cells_memory2.1256e-030.2150image
ENSG00000109475.15,RPL34LGGEAGB_cells_memory8.7135e-030.1806image
ENSG00000109475.15,RPL34LUSCEAGT_cells_follicular_helper8.0168e-030.3167image
chr4:108623035-108623665:+OVEERT_cells_gamma_delta3.6180e-020.3504image
ENSG00000109475.15,RPL34OVEAGMonocytes1.3907e-020.2793image
chr4:108625466-108629008:+PRADEERT_cells_CD4_memory_resting4.3412e-02-0.1921image
ENSG00000109475.15,RPL34PRADEAGMonocytes4.4511e-02-0.1660image
ENSG00000109475.15,RPL34SKCMEAGNK_cells_resting5.5476e-030.4306image
chr4:108623035-108623665:+STADEERMacrophages_M11.5279e-020.1744image
chr4:108625466-108629008:+THCAEERMonocytes3.3011e-020.2734image


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6. Enriched editing regions and immune gene sets for RPL34


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
chr4:108623035-108623665:+STADEER2.8225e-020.15802.8005e-020.15826.5997e-030.19491.5829e-040.2686image


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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
ENSG00000109475.15,RPL34BLCAGSVA_HALLMARK_ANGIOGENESISEAG6.6985e-030.3436image
chr4:108623035-108623665:+BLCAGSVA_HALLMARK_ANGIOGENESISEER7.3926e-030.3425image
chr4:108625466-108629008:+BRCAGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEER3.5547e-030.3392image
ENSG00000109475.15,RPL34CESCGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG1.2826e-030.5442image
chr4:108623035-108623665:+ESCAGSVA_HALLMARK_KRAS_SIGNALING_UPEER3.3455e-02-0.2003image
ENSG00000109475.15,RPL34ESCAGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG2.2765e-02-0.2078image
ENSG00000109475.15,RPL34HNSCGSVA_HALLMARK_UV_RESPONSE_DNEAG4.6173e-02-0.4293image
chr4:108625466-108629008:+LGGGSVA_HALLMARK_G2M_CHECKPOINTEER5.6483e-04-0.2405image
ENSG00000109475.15,RPL34LGGGSVA_HALLMARK_PROTEIN_SECRETIONEAG4.0323e-04-0.2420image
chr4:108623035-108623665:+LUADGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER1.0291e-03-0.4166image
ENSG00000109475.15,RPL34LUADGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG4.2912e-03-0.3607image
ENSG00000109475.15,RPL34LUSCGSVA_HALLMARK_DNA_REPAIREAG4.9002e-020.2379image
chr4:108625466-108629008:+OVGSVA_HALLMARK_COAGULATIONEER6.4457e-030.4138image
chr4:108623035-108623665:+OVGSVA_HALLMARK_PANCREAS_BETA_CELLSEER3.3096e-02-0.3560image
ENSG00000109475.15,RPL34PAADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG4.8145e-020.4074image
chr4:108625466-108629008:+PRADGSVA_HALLMARK_TGF_BETA_SIGNALINGEER7.6369e-03-0.2520image
chr4:108625466-108629008:+STADGSVA_HALLMARK_BILE_ACID_METABOLISMEER4.4437e-020.2562image
ENSG00000109475.15,RPL34STADGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG8.0622e-060.2978image
chr4:108623035-108623665:+STADGSVA_HALLMARK_TGF_BETA_SIGNALINGEER4.2483e-060.3242image
ENSG00000109475.15,RPL34THCAGSVA_HALLMARK_FATTY_ACID_METABOLISMEAG2.8537e-02-0.2169image


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7. Enriched editing regions and drugs for RPL34


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
ENSG00000109475.15,RPL34BLCAATRAEAG8.0781e-040.4178image
chr4:108623035-108623665:+BLCAATRAEER9.1480e-040.4171image
ENSG00000109475.15,RPL34BRCABMS.708163EAG4.1612e-020.1480image
ENSG00000109475.15,RPL34CESCAZD6244EAG3.5979e-02-0.3721image
ENSG00000109475.15,RPL34COADEmbelinEAG2.0747e-02-0.3789image
chr4:108623035-108623665:+COADEmbelinEER2.0747e-02-0.3789image
chr4:108623035-108623665:+ESCABosutinibEER1.3211e-02-0.2325image
ENSG00000109475.15,RPL34ESCABosutinibEAG5.2102e-03-0.2535image
chr4:108625466-108629008:+ESCAGNF.2EER7.1006e-03-0.5569image
ENSG00000109475.15,RPL34HNSCA.443654EAG3.8970e-03-0.5894image
chr4:108623035-108623665:+KIRCJNK.9LEER1.5818e-020.4774image
ENSG00000109475.15,RPL34KIRCBMS.708163EAG1.3349e-030.5078image
ENSG00000109475.15,RPL34LAMLCisplatinEAG1.2173e-02-0.2633image
chr4:108625466-108629008:+LGGGemcitabineEER3.4972e-030.2046image
ENSG00000109475.15,RPL34LGGEmbelinEAG1.2902e-060.3268image
chr4:108623035-108623665:+LUADKIN001.135EER5.6567e-050.4994image
ENSG00000109475.15,RPL34LUADKIN001.135EAG6.7808e-050.4874image
ENSG00000109475.15,RPL34LUSCEpothilone.BEAG2.0642e-02-0.2782image
chr4:108625466-108629008:+OVCMKEER8.4914e-03-0.4010image
ENSG00000109475.15,RPL34PRADEmbelinEAG4.8053e-020.1634image
chr4:108625466-108629008:+PRADEHT.1864EER1.6673e-02-0.2268image
ENSG00000109475.15,RPL34SKCMAS601245EAG2.2892e-02-0.3590image
chr4:108625466-108629008:+STADMethotrexateEER3.0647e-020.2748image
ENSG00000109475.15,RPL34STADBicalutamideEAG8.4551e-04-0.2250image
chr4:108623035-108623665:+STADAS601245EER1.0466e-02-0.1839image
ENSG00000109475.15,RPL34THCAAZD7762EAG2.9076e-02-0.2162image


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