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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: RPS9 (ImmuneEditome ID:6203)

1. Gene summary of enriched editing regions for RPS9

check button Gene summary
Gene informationGene symbol

RPS9

Gene ID

6203

GeneSynonymsS9|uS4
GeneCytomap

19q13.42

GeneTypeprotein-coding
GeneDescription40S ribosomal protein S9|small ribosomal subunit protein uS4
GeneModificationdate20230517
UniprotIDP46781;F2Z3C0;C9JM19;A8MXK4;B5MCT8;A0A024R4M0
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr19:54202074-54204660:+ENST00000484121.4ENSG00000170889.12RPS9ncRNA_intronicAluSp,L1MB2,L2a,AluSz,AluSx,AluSz6,AluJbchr19:54202074-54204660:+.alignment
chr19:54202074-54204660:+ENST00000495002.4ENSG00000170889.12RPS9ncRNA_intronicAluSp,L1MB2,L2a,AluSz,AluSx,AluSz6,AluJbchr19:54202074-54204660:+.alignment
chr19:54212099-54213326:+ENST00000448962.4ENSG00000170889.12RPS9intronicL1MB5,AluSz,AluJo,AluSxchr19:54212099-54213326:+.alignment


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2. Tumor-specific enriched editing regions for RPS9


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


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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
ENSG00000170889.12,RPS9HNSCEAG2.6584e-024.8580e-022.1833e-10image
chr19:54202074-54204660:+LUADEER4.5053e-022.2094e-024.6193e+01image

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3. Enriched editing regions and immune related genes for RPS9


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
chr19:54202074-54204660:+ESCAEERENSG00000140479,PCSK6-0.46991.7577e-042.3344e-07-0.4494imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+ESCAEERENSG00000128833,MYO5C-0.44305.3466e-042.7723e-06-0.4113imageNNNAB_cells_naiveGSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+ESCAEERENSG00000047230,CTPS2-0.43619.2734e-045.0492e-07-0.4380imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_P53_PATHWAY
chr19:54202074-54204660:+ESCAEERENSG00000140455,USP3-0.42799.3350e-047.3322e-07-0.4324imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_HYPOXIA
chr19:54202074-54204660:+ESCAEERENSG00000176171,BNIP30.42211.1940e-037.3718e-070.4323imageNNBNIP3T_cells_regulatory_(Tregs)GSVA_HALLMARK_HYPOXIA
chr19:54202074-54204660:+ESCAEERENSG00000131966,ACTR100.42171.4119e-038.6862e-070.4298imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION
chr19:54202074-54204660:+ESCAEERENSG00000181031,RPH3AL-0.41661.4776e-031.2261e-06-0.4244imageNNRPH3ALT_cells_regulatory_(Tregs)GSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+ESCAEERENSG00000236060,HSPB1P10.41321.7458e-034.4180e-070.4400imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_P53_PATHWAY
chr19:54202074-54204660:+ESCAEERENSG00000178409,BEND3-0.41651.9833e-032.7958e-06-0.4112imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_MYOGENESIS
chr19:54202074-54204660:+ESCAEERENSG00000228594,C1orf2330.38862.9365e-034.7126e-060.4025imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_KRAS_SIGNALING_DN
chr19:54202074-54204660:+ESCAEERENSG00000140479,PCSK6-0.46991.7577e-042.3344e-07-0.4494imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+ESCAEERENSG00000128833,MYO5C-0.44305.3466e-042.7723e-06-0.4113imageNNNAB_cells_naiveGSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+ESCAEERENSG00000047230,CTPS2-0.43619.2734e-045.0492e-07-0.4380imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_P53_PATHWAY
chr19:54202074-54204660:+ESCAEERENSG00000140455,USP3-0.42799.3350e-047.3322e-07-0.4324imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_HYPOXIA
chr19:54202074-54204660:+ESCAEERENSG00000176171,BNIP30.42211.1940e-037.3718e-070.4323imageNNBNIP3T_cells_regulatory_(Tregs)GSVA_HALLMARK_HYPOXIA
chr19:54202074-54204660:+ESCAEERENSG00000131966,ACTR100.42171.4119e-038.6862e-070.4298imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION
chr19:54202074-54204660:+ESCAEERENSG00000181031,RPH3AL-0.41661.4776e-031.2261e-06-0.4244imageNNRPH3ALT_cells_regulatory_(Tregs)GSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+ESCAEERENSG00000236060,HSPB1P10.41321.7458e-034.4180e-070.4400imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_P53_PATHWAY
chr19:54202074-54204660:+ESCAEERENSG00000178409,BEND3-0.41651.9833e-032.7958e-06-0.4112imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_MYOGENESIS
chr19:54202074-54204660:+ESCAEERENSG00000228594,C1orf2330.38862.9365e-034.7126e-060.4025imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_KRAS_SIGNALING_DN

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4. Enriched editing regions and immune related splicing for RPS9


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
chr19:54202074-54204660:+
ESCAEERESENSG00000156504.12chrX134771161:134771354:134772142:134772283:134781820:134781917-0.36762.0095e-026.9329e-06-0.4157imageNNNAT_cells_gamma_deltaGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALING
chr19:54202074-54204660:+
ESCAEERESENSG00000095637.16chr1095410632:95410777:95414493:95414862:95421960:954220730.34022.5111e-022.2604e-060.4569imageNNNADendritic_cells_restingGSVA_HALLMARK_MYOGENESIS
chr19:54202074-54204660:+
ESCAEERIRENSG00000213648.6chr1629463344:29463471:29463566:294636610.38492.5651e-022.2879e-060.4145imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+
ESCAEERIRENSG00000055950.12chr10100981375:100983817:100983947:100984074-0.34424.8174e-029.8635e-06-0.4042imageNNNAT_cells_CD4_memory_restingGSVA_HALLMARK_BILE_ACID_METABOLISM
chr19:54202074-54204660:+
ESCAEERESENSG00000140254.8chr1545120795:45120805:45121086:45121221:45122184:451222400.33342.2690e-021.5985e-050.4470imageNNNAT_cells_CD8GSVA_HALLMARK_HYPOXIA
chr19:54202074-54204660:+
ESCAEERMEXENSG00000197249.8chr1494378448:94378640:94379463:94379611:94382958:94383241:94388559:943885890.37662.3183e-022.7677e-060.4114imageNNSERPINA1T_cells_regulatory_(Tregs)GSVA_HALLMARK_BILE_ACID_METABOLISM

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5. Enriched editing regions and immune infiltration for RPS9


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
ENSG00000170889.12,RPS9BLCAEAGNK_cells_resting1.0268e-020.3465image
ENSG00000170889.12,RPS9BRCAEAGPlasma_cells2.7737e-020.1674image
ENSG00000170889.12,RPS9CESCEAGB_cells_memory3.0319e-02-0.3346image
chr19:54202074-54204660:+COADEERDendritic_cells_activated4.0794e-020.3379image
ENSG00000170889.12,RPS9COADEAGT_cells_CD4_memory_resting2.5986e-02-0.3001image
chr19:54202074-54204660:+ESCAEERT_cells_regulatory_(Tregs)5.2390e-03-0.2523image
ENSG00000170889.12,RPS9ESCAEAGT_cells_regulatory_(Tregs)2.7613e-04-0.3116image
ENSG00000170889.12,RPS9HNSCEAGNK_cells_resting1.8294e-040.6696image
chr19:54202074-54204660:+KIRCEERT_cells_CD81.8686e-020.3848image
ENSG00000170889.12,RPS9KIRCEAGDendritic_cells_resting2.8829e-020.3297image
chr19:54202074-54204660:+LAMLEERMacrophages_M22.7746e-02-0.2001image
ENSG00000170889.12,RPS9LAMLEAGMacrophages_M21.1794e-02-0.2228image
chr19:54202074-54204660:+LUSCEERNK_cells_activated2.7729e-030.2933image
ENSG00000170889.12,RPS9LUSCEAGDendritic_cells_resting2.0081e-02-0.2014image
chr19:54202074-54204660:+OVEERT_cells_CD4_memory_activated1.2314e-020.3161image
ENSG00000170889.12,RPS9OVEAGT_cells_CD4_memory_activated2.9551e-020.2199image
ENSG00000170889.12,RPS9SKCMEAGT_cells_CD4_memory_activated4.7707e-02-0.2968image
chr19:54202074-54204660:+STADEERT_cells_gamma_delta1.1612e-020.1818image
ENSG00000170889.12,RPS9STADEAGT_cells_CD4_memory_resting2.3569e-02-0.1551image
ENSG00000170889.12,RPS9TGCTEAGB_cells_memory1.3892e-040.7241image


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6. Enriched editing regions and immune gene sets for RPS9


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
ENSG00000170889.12,RPS9BLCAGSVA_HALLMARK_SPERMATOGENESISEAG3.4887e-020.2877image
ENSG00000170889.12,RPS9BRCAGSVA_HALLMARK_ANDROGEN_RESPONSEEAG2.4850e-020.1706image
ENSG00000170889.12,RPS9CESCGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG2.6481e-02-0.3423image
chr19:54202074-54204660:+COADGSVA_HALLMARK_APICAL_SURFACEEER1.4578e-020.3985image
ENSG00000170889.12,RPS9COADGSVA_HALLMARK_KRAS_SIGNALING_DNEAG8.0399e-030.3539image
ENSG00000170889.12,RPS9ESCAGSVA_HALLMARK_BILE_ACID_METABOLISMEAG1.2360e-02-0.2172image
chr19:54202074-54204660:+ESCAGSVA_HALLMARK_HYPOXIAEER1.1845e-020.2281image
ENSG00000170889.12,RPS9HNSCGSVA_HALLMARK_KRAS_SIGNALING_DNEAG1.8392e-02-0.4588image
chr19:54202074-54204660:+KIRCGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER2.7192e-030.4788image
ENSG00000170889.12,RPS9LAMLGSVA_HALLMARK_G2M_CHECKPOINTEAG1.2226e-04-0.3343image
chr19:54202074-54204660:+LAMLGSVA_HALLMARK_G2M_CHECKPOINTEER5.5551e-04-0.3093image
chr19:54202074-54204660:+LUADGSVA_HALLMARK_HYPOXIAEER7.3225e-030.2174image
ENSG00000170889.12,RPS9LUADGSVA_HALLMARK_PROTEIN_SECRETIONEAG2.9666e-040.2645image
chr19:54202074-54204660:+LUSCGSVA_HALLMARK_GLYCOLYSISEER1.7353e-020.2352image
ENSG00000170889.12,RPS9LUSCGSVA_HALLMARK_NOTCH_SIGNALINGEAG1.2213e-020.2168image
ENSG00000170889.12,RPS9OVGSVA_HALLMARK_HEME_METABOLISMEAG4.7368e-02-0.2008image
chr19:54202074-54204660:+OVGSVA_HALLMARK_PANCREAS_BETA_CELLSEER1.0166e-030.4073image
ENSG00000170889.12,RPS9PRADGSVA_HALLMARK_ANDROGEN_RESPONSEEAG4.0403e-040.5582image
chr19:54202074-54204660:+STADGSVA_HALLMARK_DNA_REPAIREER1.0280e-030.2351image
ENSG00000170889.12,RPS9STADGSVA_HALLMARK_DNA_REPAIREAG1.5573e-020.1656image
ENSG00000170889.12,RPS9TGCTGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG5.2909e-030.5732image


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7. Enriched editing regions and drugs for RPS9


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
ENSG00000170889.12,RPS9BLCACI.1040EAG5.3368e-040.4558image
ENSG00000170889.12,RPS9BRCAAICAREAG9.9344e-030.1955image
chr19:54202074-54204660:+COADMethotrexateEER2.2549e-020.3741image
ENSG00000170889.12,RPS9COADBexaroteneEAG2.7338e-03-0.3964image
ENSG00000170889.12,RPS9ESCACGP.082996EAG5.8113e-04-0.2955image
chr19:54202074-54204660:+ESCACGP.082996EER4.2779e-05-0.3630image
chr19:54202074-54204660:+KIRCCCT018159EER1.9755e-02-0.3817image
ENSG00000170889.12,RPS9LAMLBIRB.0796EAG1.2381e-03-0.2835image
chr19:54202074-54204660:+LAMLLFM.A13EER5.9547e-04-0.3077image
chr19:54202074-54204660:+LUADDocetaxelEER4.9249e-03-0.2277image
ENSG00000170889.12,RPS9LUADBMS.754807EAG2.1975e-02-0.1693image
ENSG00000170889.12,RPS9OVBMS.708163EAG2.6062e-020.2248image
chr19:54202074-54204660:+OVMG.132EER3.1344e-03-0.3693image
chr19:54202074-54204660:+STADLapatinibEER5.1646e-03-0.2021image
ENSG00000170889.12,RPS9STADMG.132EAG2.1214e-02-0.1578image
ENSG00000170889.12,RPS9TGCTCHIR.99021EAG3.3977e-03-0.5963image


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