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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: ATP1B3 (ImmuneEditome ID:483)

1. Gene summary of enriched editing regions for ATP1B3

check button Gene summary
Gene informationGene symbol

ATP1B3

Gene ID

483

GeneSynonymsATPB-3|CD298
GeneCytomap

3q23

GeneTypeprotein-coding
GeneDescriptionsodium/potassium-transporting ATPase subunit beta-3|ATPase, Na+/K+ transporting, beta 3 polypeptide|Na, K-ATPase beta-3 polypeptide|sodium pump subunit beta-3|sodium-potassium ATPase subunit beta 3 (non-catalytic)|sodium/potassium-dependent ATPase subunit beta-3|sodium/potassium-transporting ATPase beta-3 chain
GeneModificationdate20230329
UniprotIDP54709;F8WBY4;C9J6S2;H7C4L9;C9JA36;C9JXZ1
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr3:141882615-141883492:+ENST00000286371.6ENSG00000069849.9ATP1B3intronicAluSp,AluJb,L2chr3:141882615-141883492:+.alignment
chr3:141882615-141883492:+ENST00000462082.1ENSG00000069849.9ATP1B3intronicAluSp,AluJb,L2chr3:141882615-141883492:+.alignment
chr3:141882615-141883492:+ENST00000465172.4ENSG00000069849.9ATP1B3intronicAluSp,AluJb,L2chr3:141882615-141883492:+.alignment
chr3:141882615-141883492:+ENST00000466678.4ENSG00000069849.9ATP1B3intronicAluSp,AluJb,L2chr3:141882615-141883492:+.alignment
chr3:141882615-141883492:+ENST00000475483.4ENSG00000069849.9ATP1B3intronicAluSp,AluJb,L2chr3:141882615-141883492:+.alignment
chr3:141882615-141883492:+ENST00000495216.1ENSG00000069849.9ATP1B3intronicAluSp,AluJb,L2chr3:141882615-141883492:+.alignment
chr3:141889133-141889692:+ENST00000286371.6ENSG00000069849.9ATP1B3intronicTHE1D,L1ME3G,AluSqchr3:141889133-141889692:+.alignment
chr3:141889133-141889692:+ENST00000462082.1ENSG00000069849.9ATP1B3intronicTHE1D,L1ME3G,AluSqchr3:141889133-141889692:+.alignment
chr3:141889133-141889692:+ENST00000465172.4ENSG00000069849.9ATP1B3intronicTHE1D,L1ME3G,AluSqchr3:141889133-141889692:+.alignment
chr3:141889133-141889692:+ENST00000466678.4ENSG00000069849.9ATP1B3intronicTHE1D,L1ME3G,AluSqchr3:141889133-141889692:+.alignment
chr3:141889133-141889692:+ENST00000475483.4ENSG00000069849.9ATP1B3intronicTHE1D,L1ME3G,AluSqchr3:141889133-141889692:+.alignment
chr3:141889133-141889692:+ENST00000495216.1ENSG00000069849.9ATP1B3intronicTHE1D,L1ME3G,AluSqchr3:141889133-141889692:+.alignment
chr3:141916892-141917684:+ENST00000482635.1ENSG00000069849.9ATP1B3ncRNA_intronicMIR1_Amn,MER5A,AluY,AluScchr3:141916892-141917684:+.alignment
chr3:141919684-141920531:+ENST00000482635.1ENSG00000069849.9ATP1B3ncRNA_intronicAluSz6,AluSxchr3:141919684-141920531:+.alignment


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2. Tumor-specific enriched editing regions for ATP1B3


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
chr3:141919684-141920531:+HNSCCliEER3.5572e-021.0484e-02-0.5458image


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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 ATP1B3


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 ATP1B3


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
chr3:141919684-141920531:+
ESCAEERIRENSG00000172243.13chr1210116776:10117523:10118461:10118590-0.25703.0103e-021.1305e-05-0.4275imageNFUS;SRSF1;U2AF2CLEC7AMast_cells_restingGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE
chr3:141919684-141920531:+
ESCAEERIRENSG00000011422.7chr1943656478:43656640:43660973:43661324-0.42285.2904e-045.0396e-05-0.4159imageNFUS;HNRNPK;KHSRP;NOP58;PCBP2;PTBP1;RBFOX2;SRSF1;TARDBP;TIAL1;U2AF1;U2AF2;UPF1PLAURGSVA_HALLMARK_GLYCOLYSIS
ENSG00000069849.9,ATP1B3
ESCAEAGIRENSG00000011422.7chr1943656478:43656640:43660973:43661324-0.41565.9773e-042.0584e-05-0.4282imageNADAR;BUD13;CNBP;CPSF6;CSTF2T;DDX3X;DDX42;DGCR8;DHX9;EIF4A3;EIF4G2;ELAVL1;FAM120A;FBL;FMR1;FUS;FXR2;GTF2F1;HNRNPA1;HNRNPC;HNRNPK;HNRNPM;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;ILF3;KHSRP;LARP4B;LARP7;LIN28;LIN28B;LSM11;MOV10;MSI1;NOP56;NOP58;NUMA1;PCBP2;PRPF8;PTBP1;QKI;RBFOX2;RBM10;RBM47;SLTM;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARBP2;TARDBP;TIA1;TIAL1;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;XRN2;YTHDF1;YWHAG;ZNF184PLAURGSVA_HALLMARK_GLYCOLYSIS

More results



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5. Enriched editing regions and immune infiltration for ATP1B3


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
chr3:141916892-141917684:+HNSCEERMacrophages_M05.9134e-030.5345image
ENSG00000069849.9,ATP1B3HNSCEAGB_cells_naive4.8592e-02-0.3265image
ENSG00000069849.9,ATP1B3LAMLEAGDendritic_cells_activated7.3720e-030.3345image
chr3:141919684-141920531:+LUSCEERT_cells_gamma_delta3.5877e-030.2718image
chr3:141919684-141920531:+OVEERMacrophages_M21.8321e-020.4146image
ENSG00000069849.9,ATP1B3OVEAGMacrophages_M25.8931e-030.4042image
chr3:141919684-141920531:+PCPGEERMast_cells_resting2.2274e-040.7087image
ENSG00000069849.9,ATP1B3PCPGEAGMast_cells_resting1.6851e-030.5755image
chr3:141889133-141889692:+STADEERT_cells_regulatory_(Tregs)2.2761e-02-0.4078image
chr3:141919684-141920531:+STADEERMacrophages_M06.0020e-050.3682image
ENSG00000069849.9,ATP1B3STADEAGMacrophages_M02.1094e-040.3031image


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6. Enriched editing regions and immune gene sets for ATP1B3


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
chr3:141889133-141889692:+ESCAGSVA_HALLMARK_MYC_TARGETS_V1EER1.9851e-02-0.3285image
chr3:141919684-141920531:+ESCAGSVA_HALLMARK_PROTEIN_SECRETIONEER4.3466e-030.2597image
ENSG00000069849.9,ATP1B3ESCAGSVA_HALLMARK_PROTEIN_SECRETIONEAG4.1022e-030.2571image
ENSG00000069849.9,ATP1B3HNSCGSVA_HALLMARK_ADIPOGENESISEAG2.0604e-030.4904image
chr3:141919684-141920531:+HNSCGSVA_HALLMARK_P53_PATHWAYEER1.8199e-020.5099image
chr3:141916892-141917684:+HNSCGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER5.0929e-040.6443image
ENSG00000069849.9,ATP1B3KIRCGSVA_HALLMARK_NOTCH_SIGNALINGEAG1.8117e-02-0.5225image
chr3:141919684-141920531:+LUSCGSVA_HALLMARK_PROTEIN_SECRETIONEER5.3350e-030.2604image
ENSG00000069849.9,ATP1B3LUSCGSVA_HALLMARK_PROTEIN_SECRETIONEAG1.1424e-020.2212image
chr3:141919684-141920531:+OVGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER3.9647e-020.3656image
ENSG00000069849.9,ATP1B3OVGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG1.7578e-020.3524image
ENSG00000069849.9,ATP1B3PCPGGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEAG1.3973e-03-0.5836image
chr3:141919684-141920531:+PCPGGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEER6.3253e-03-0.5634image
chr3:141919684-141920531:+STADGSVA_HALLMARK_MITOTIC_SPINDLEEER7.0537e-030.2522image
ENSG00000069849.9,ATP1B3STADGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG2.3791e-020.1877image
chr3:141889133-141889692:+STADGSVA_HALLMARK_BILE_ACID_METABOLISMEER2.0592e-020.4140image


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7. Enriched editing regions and drugs for ATP1B3


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
chr3:141889133-141889692:+ESCAAS601245EER6.8282e-03-0.3778image
ENSG00000069849.9,ATP1B3ESCAFH535EAG4.3365e-02-0.1825image
chr3:141882615-141883492:+ESCAMetforminEER1.9518e-02-0.5051image
ENSG00000069849.9,ATP1B3HNSCATRAEAG3.4007e-030.4691image
chr3:141919684-141920531:+HNSCAZD.0530EER2.1590e-02-0.4980image
chr3:141916892-141917684:+HNSCBAY.61.3606EER3.9094e-050.7266image
ENSG00000069849.9,ATP1B3LAMLBleomycinEAG1.6230e-020.3018image
chr3:141882615-141883492:+LAMLCCT018159EER1.5955e-02-0.4678image
chr3:141919684-141920531:+LUSCBMS.754807EER7.4352e-03-0.2506image
ENSG00000069849.9,ATP1B3LUSCKIN001.135EAG3.9760e-03-0.2510image
chr3:141919684-141920531:+OVMidostaurinEER1.6186e-020.4218image
ENSG00000069849.9,ATP1B3OVAUY922EAG1.8113e-02-0.3509image
ENSG00000069849.9,ATP1B3PCPGBI.D1870EAG1.1775e-02-0.4775image
chr3:141919684-141920531:+PCPGABT.888EER2.9771e-02-0.4636image
chr3:141919684-141920531:+STADAG.014699EER5.0097e-030.2623image
ENSG00000069849.9,ATP1B3STADAG.014699EAG5.8504e-040.2822image
chr3:141889133-141889692:+STADBleomycinEER5.9808e-040.5817image


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check button EAGs targeted by drugs from DrugBank database.
* EAG: EER-associated genes.
EERENSTUniprotIDDrugBankIDDrugDrugType
chr3:141882615-141883492:+ENST00000286371.6P54709DB09020BisacodylSmallMoleculeDrug
chr3:141889133-141889692:+ENST00000286371.6P54709DB09020BisacodylSmallMoleculeDrug