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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: PGK1 (ImmuneEditome ID:5230)

1. Gene summary of enriched editing regions for PGK1

check button Gene summary
Gene informationGene symbol

PGK1

Gene ID

5230

GeneSynonymsHEL-S-68p|MIG10|PGKA
GeneCytomap

Xq21.1

GeneTypeprotein-coding
GeneDescriptionphosphoglycerate kinase 1|PRP 2|cell migration-inducing gene 10 protein|epididymis secretory sperm binding protein Li 68p|primer recognition protein 2
GeneModificationdate20230521
UniprotIDP00558
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chrX:78120507-78120779:+ENST00000491291.1ENSG00000102144.12PGK1ncRNA_intronicAluJbchrX:78120507-78120779:+.alignment
chrX:78121918-78122202:+ENST00000491291.1ENSG00000102144.12PGK1ncRNA_intronicAluJochrX:78121918-78122202:+.alignment
chrX:78128310-78129162:+ENST00000373316.4ENSG00000102144.12PGK1UTR3L1ME4b,AluSx,AluYchrX:78128310-78129162:+.alignment


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2. Tumor-specific enriched editing regions for PGK1


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
chrX:78120507-78120779:+KIRCEER3.2835e-032.2997e-031.4440e+06image
chrX:78121918-78122202:+OVEER9.8054e-033.4656e-022.3491e-02image

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3. Enriched editing regions and immune related genes for PGK1


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 PGK1


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
ENSG00000102144.12,PGK1
ESCAEAGIRENSG00000170545.12chr1251245851:51246051:51246750:51246831-0.28962.4771e-023.2404e-06-0.4136imageNADAR;BUD13;CELF2;CNBP;CPSF6;CSTF2T;DDX3X;DDX54;DHX9;DKC1;EIF4A3;ELAVL1;EWSR1;FAM120A;FBL;FUS;FXR1;GTF2F1;HNRNPA1;HNRNPC;HNRNPK;HNRNPL;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;ILF3;KHDRBS1;KHSRP;LARP7;LIN28A;LIN28B;MOV10;NOP56;NOP58;PCBP2;PRPF8;PTBP1;QKI;RBFOX2;RBM22;RBM27;RBM47;SAFB2;SLTM;SND1;SRSF1;SRSF3;TAF15;TARBP2;TARDBP;TNRC6A;TROVE2;U2AF2;UPF1;YTHDF1;YWHAG;ZNF184SMAGPGSVA_HALLMARK_MYOGENESIS

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5. Enriched editing regions and immune infiltration for PGK1


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
ENSG00000102144.12,PGK1ACCEAGMacrophages_M25.1664e-04-0.6915image
chrX:78121918-78122202:+BLCAEERT_cells_CD4_memory_activated1.8762e-020.3796image
chrX:78121918-78122202:+BRCAEERT_cells_CD4_naive1.3841e-030.4443image
ENSG00000102144.12,PGK1BRCAEAGT_cells_CD4_naive5.8418e-040.2732image
chrX:78121918-78122202:+CESCEERT_cells_CD4_memory_activated3.5293e-02-0.3677image
chrX:78121918-78122202:+COADEERT_cells_CD4_memory_resting1.3493e-030.5346image
ENSG00000102144.12,PGK1COADEAGT_cells_CD4_memory_resting1.8014e-030.4727image
chrX:78121918-78122202:+ESCAEERNK_cells_activated4.5496e-020.2091image
ENSG00000102144.12,PGK1ESCAEAGEosinophils4.9154e-02-0.1808image
chrX:78121918-78122202:+GBMEEREosinophils7.5259e-030.5657image
ENSG00000102144.12,PGK1GBMEAGT_cells_gamma_delta3.3354e-02-0.2109image
chrX:78121918-78122202:+KIRCEERPlasma_cells1.1257e-020.2136image
ENSG00000102144.12,PGK1KIRCEAGPlasma_cells1.7164e-030.2237image
ENSG00000102144.12,PGK1KIRPEAGNK_cells_activated1.6293e-020.3924image
chrX:78120507-78120779:+LUADEERT_cells_CD84.5907e-020.4400image
chrX:78121918-78122202:+LUADEERMacrophages_M01.5032e-02-0.3100image
ENSG00000102144.12,PGK1LUADEAGB_cells_naive1.3735e-020.2604image
ENSG00000102144.12,PGK1PCPGEAGMast_cells_resting2.4233e-020.3650image
ENSG00000102144.12,PGK1SARCEAGPlasma_cells1.7149e-020.5025image
chrX:78121918-78122202:+STADEERDendritic_cells_resting4.4564e-030.2767image
chrX:78128310-78129162:+STADEERT_cells_CD4_memory_resting1.9444e-03-0.2570image
ENSG00000102144.12,PGK1STADEAGT_cells_CD4_memory_activated1.8989e-030.2167image
ENSG00000102144.12,PGK1THCAEAGNeutrophils1.2414e-040.6035image


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6. Enriched editing regions and immune gene sets for PGK1


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
ENSG00000102144.12,PGK1ACCGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG1.3815e-02-0.5283image
ENSG00000102144.12,PGK1BLCAGSVA_HALLMARK_UV_RESPONSE_DNEAG3.2241e-03-0.4208image
chrX:78121918-78122202:+BLCAGSVA_HALLMARK_KRAS_SIGNALING_DNEER4.5082e-020.3270image
chrX:78121918-78122202:+BRCAGSVA_HALLMARK_PEROXISOMEEER1.8222e-030.4343image
ENSG00000102144.12,PGK1BRCAGSVA_HALLMARK_HEDGEHOG_SIGNALINGEAG4.5592e-030.2267image
ENSG00000102144.12,PGK1CESCGSVA_HALLMARK_SPERMATOGENESISEAG3.9094e-030.4571image
chrX:78121918-78122202:+CESCGSVA_HALLMARK_DNA_REPAIREER1.7479e-030.5240image
chrX:78121918-78122202:+COADGSVA_HALLMARK_G2M_CHECKPOINTEER7.5495e-03-0.4567image
ENSG00000102144.12,PGK1COADGSVA_HALLMARK_G2M_CHECKPOINTEAG1.5914e-03-0.4776image
chrX:78121918-78122202:+ESCAGSVA_HALLMARK_SPERMATOGENESISEER8.5869e-040.3417image
ENSG00000102144.12,PGK1ESCAGSVA_HALLMARK_SPERMATOGENESISEAG2.2862e-030.2770image
ENSG00000102144.12,PGK1GBMGSVA_HALLMARK_KRAS_SIGNALING_DNEAG4.5298e-03-0.2789image
chrX:78128310-78129162:+GBMGSVA_HALLMARK_KRAS_SIGNALING_DNEER2.6220e-02-0.2305image
ENSG00000102144.12,PGK1HNSCGSVA_HALLMARK_SPERMATOGENESISEAG1.1769e-02-0.4692image
ENSG00000102144.12,PGK1KIRCGSVA_HALLMARK_UV_RESPONSE_DNEAG1.5516e-02-0.1735image
chrX:78121918-78122202:+KIRCGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER1.0469e-040.3220image
ENSG00000102144.12,PGK1KIRPGSVA_HALLMARK_ANDROGEN_RESPONSEEAG5.3966e-04-0.5414image
ENSG00000102144.12,PGK1LGGGSVA_HALLMARK_ANGIOGENESISEAG2.8136e-030.2704image
chrX:78121918-78122202:+LUADGSVA_HALLMARK_MYOGENESISEER4.5207e-020.2574image
chrX:78120507-78120779:+LUSCGSVA_HALLMARK_MTORC1_SIGNALINGEER1.6608e-020.4653image
ENSG00000102144.12,PGK1LUSCGSVA_HALLMARK_G2M_CHECKPOINTEAG2.6646e-030.3097image
chrX:78121918-78122202:+LUSCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEER3.8753e-040.4044image
chrX:78121918-78122202:+OVGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER2.9115e-030.3328image
ENSG00000102144.12,PGK1OVGSVA_HALLMARK_DNA_REPAIREAG4.0454e-02-0.1874image
ENSG00000102144.12,PGK1PAADGSVA_HALLMARK_KRAS_SIGNALING_DNEAG9.5950e-040.5142image
chrX:78121918-78122202:+PAADGSVA_HALLMARK_KRAS_SIGNALING_DNEER1.8523e-040.6400image
ENSG00000102144.12,PGK1PCPGGSVA_HALLMARK_MITOTIC_SPINDLEEAG1.2515e-02-0.4013image
ENSG00000102144.12,PGK1SARCGSVA_HALLMARK_MITOTIC_SPINDLEEAG9.6549e-03-0.5389image
ENSG00000102144.12,PGK1SKCMGSVA_HALLMARK_UV_RESPONSE_DNEAG2.3416e-04-0.4934image
chrX:78128310-78129162:+STADGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER1.4798e-030.2634image
ENSG00000102144.12,PGK1STADGSVA_HALLMARK_UV_RESPONSE_DNEAG5.5721e-03-0.1939image
chrX:78121918-78122202:+STADGSVA_HALLMARK_G2M_CHECKPOINTEER2.5054e-02-0.2197image


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7. Enriched editing regions and drugs for PGK1


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
ENSG00000102144.12,PGK1ACCAP.24534EAG6.9955e-030.5699image
ENSG00000102144.12,PGK1BLCAKIN001.135EAG1.4610e-020.3541image
chrX:78121918-78122202:+BLCAGDC.0449EER3.0045e-02-0.3523image
chrX:78121918-78122202:+BRCAABT.263EER3.8385e-040.4873image
ENSG00000102144.12,PGK1BRCABryostatin.1EAG3.0629e-02-0.1737image
ENSG00000102144.12,PGK1CESCCI.1040EAG4.8046e-040.5390image
chrX:78121918-78122202:+CESCCI.1040EER8.7497e-040.5517image
ENSG00000102144.12,PGK1COADEpothilone.BEAG5.1604e-030.4287image
chrX:78121918-78122202:+COADCGP.082996EER1.3086e-030.5359image
ENSG00000102144.12,PGK1ESCAMG.132EAG7.1613e-03-0.2453image
chrX:78128310-78129162:+ESCAMG.132EER2.2199e-02-0.2692image
chrX:78121918-78122202:+ESCAMG.132EER1.0570e-03-0.3360image
ENSG00000102144.12,PGK1GBMBAY.61.3606EAG2.3491e-02-0.2242image
chrX:78128310-78129162:+GBMBMS.754807EER2.7347e-020.2289image
ENSG00000102144.12,PGK1HNSCEpothilone.BEAG9.7699e-030.4798image
ENSG00000102144.12,PGK1KIRCBexaroteneEAG4.7886e-050.2876image
chrX:78121918-78122202:+KIRCGDC0941EER1.1571e-03-0.2719image
ENSG00000102144.12,PGK1KIRPGDC.0449EAG1.4134e-02-0.4001image
ENSG00000102144.12,PGK1LGGCHIR.99021EAG1.5568e-04-0.3385image
chrX:78121918-78122202:+LUADMetforminEER5.4388e-030.3518image
ENSG00000102144.12,PGK1LUADBMS.754807EAG1.7873e-020.2506image
chrX:78120507-78120779:+LUSCCMKEER2.2626e-020.4453image
ENSG00000102144.12,PGK1LUSCKU.55933EAG4.8044e-030.2916image
ENSG00000102144.12,PGK1OVLFM.A13EAG8.0084e-03-0.2410image
chrX:78121918-78122202:+OVKU.55933EER3.9353e-03-0.3229image
ENSG00000102144.12,PGK1PAADKU.55933EAG5.7743e-03-0.4394image
chrX:78121918-78122202:+PAADAZD6482EER2.8779e-05-0.6949image
ENSG00000102144.12,PGK1PCPGAKT.inhibitor.VIIIEAG5.3183e-030.4432image
ENSG00000102144.12,PGK1SARCMidostaurinEAG2.5018e-03-0.6114image
ENSG00000102144.12,PGK1SKCMBexaroteneEAG1.4484e-020.3405image
chrX:78128310-78129162:+STADAICAREER3.4200e-04-0.2954image
chrX:78121918-78122202:+STADBMS.509744EER5.0854e-04-0.3350image
ENSG00000102144.12,PGK1STADMG.132EAG4.9673e-03-0.1965image
ENSG00000102144.12,PGK1THCACCT018159EAG2.0789e-02-0.3893image


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check button EAGs targeted by drugs from DrugBank database.
* EAG: EER-associated genes.
EERENSTUniprotIDDrugBankIDDrugDrugType
chrX:78128310-78129162:+ENST00000373316.4P00558DB09130CopperSmallMoleculeDrug
chrX:78128310-78129162:+ENST00000373316.4P00558DB11638ArtenimolSmallMoleculeDrug