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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: PCDHGA6 (ImmuneEditome ID:56109)

1. Gene summary of enriched editing regions for PCDHGA6

check button Gene summary
Gene informationGene symbol

PCDHGA6

Gene ID

56109

GeneSynonymsPCDH-GAMMA-A6
GeneCytomap

5q31.3

GeneTypeprotein-coding
GeneDescriptionprotocadherin gamma-A6
GeneModificationdate20230329
UniprotIDQ9Y5G7
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr5:141377328-141378451:+ENST00000610583.1ENSG00000253731.2PCDHGA6UTR3AluJo,AluSg,LTR56chr5:141377328-141378451:+.alignment
chr5:141464122-141464905:+ENST00000517434.2ENSG00000253731.2PCDHGA6intronicL1MC4a,AluJr4,AluSx1chr5:141464122-141464905:+.alignment


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2. Tumor-specific enriched editing regions for PCDHGA6


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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
ENSG00000253731.2,PCDHGA6LUADPathEAG3.6412e-029.5419e-030.4321image


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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
chr5:141377328-141378451:+OVEER2.3935e-023.9045e-025.2089e-04image

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3. Enriched editing regions and immune related genes for PCDHGA6


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

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4. Enriched editing regions and immune related splicing for PCDHGA6


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

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5. Enriched editing regions and immune infiltration for PCDHGA6


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
chr5:141377328-141378451:+BRCAEERT_cells_follicular_helper2.6917e-020.3129image
ENSG00000253731.2,PCDHGA6BRCAEAGT_cells_follicular_helper2.3614e-020.2763image
ENSG00000253731.2,PCDHGA6ESCAEAGT_cells_follicular_helper2.2142e-020.3609image
chr5:141377328-141378451:+KIRCEERDendritic_cells_resting3.1115e-02-0.2598image
ENSG00000253731.2,PCDHGA6KIRCEAGNK_cells_resting4.0015e-020.2316image
chr5:141377328-141378451:+KIRPEERB_cells_naive2.9214e-030.5808image
ENSG00000253731.2,PCDHGA6KIRPEAGB_cells_naive2.5214e-030.5312image
chr5:141377328-141378451:+LUADEERDendritic_cells_resting4.3740e-020.4150image
ENSG00000253731.2,PCDHGA6LUADEAGMast_cells_activated3.1238e-020.3756image
ENSG00000253731.2,PCDHGA6MESOEAGMacrophages_M04.4070e-02-0.3980image
chr5:141377328-141378451:+OVEERNK_cells_activated1.2975e-030.6069image
ENSG00000253731.2,PCDHGA6OVEAGT_cells_CD4_memory_activated4.9858e-050.5064image
chr5:141377328-141378451:+PRADEERMonocytes1.1403e-020.3388image
ENSG00000253731.2,PCDHGA6PRADEAGMonocytes9.3396e-040.4132image
ENSG00000253731.2,PCDHGA6SARCEAGMast_cells_activated3.1315e-040.6134image
chr5:141377328-141378451:+SKCMEERT_cells_CD4_memory_activated1.8083e-020.3974image
ENSG00000253731.2,PCDHGA6SKCMEAGT_cells_CD4_memory_activated2.0286e-020.2990image
ENSG00000253731.2,PCDHGA6STADEAGT_cells_CD4_memory_resting1.3281e-020.2989image
ENSG00000253731.2,PCDHGA6TGCTEAGT_cells_CD4_memory_activated2.1349e-020.5108image
ENSG00000253731.2,PCDHGA6THCAEAGMacrophages_M08.1383e-04-0.3106image
chr5:141377328-141378451:+THYMEERT_cells_regulatory_(Tregs)3.0284e-02-0.3896image
ENSG00000253731.2,PCDHGA6THYMEAGT_cells_regulatory_(Tregs)4.3592e-02-0.3093image


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6. Enriched editing regions and immune gene sets for PCDHGA6


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
ENSG00000253731.2,PCDHGA6BRCAGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG8.6173e-030.3185image
chr5:141377328-141378451:+BRCAGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER1.6079e-020.3388image
ENSG00000253731.2,PCDHGA6ESCAGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG3.0434e-03-0.4568image
chr5:141377328-141378451:+KIRCGSVA_HALLMARK_MITOTIC_SPINDLEEER1.0718e-02-0.3054image
chr5:141377328-141378451:+LUADGSVA_HALLMARK_MYC_TARGETS_V1EER8.9594e-030.5215image
ENSG00000253731.2,PCDHGA6LUADGSVA_HALLMARK_MYC_TARGETS_V2EAG5.4644e-040.5692image
chr5:141377328-141378451:+MESOGSVA_HALLMARK_FATTY_ACID_METABOLISMEER1.7445e-02-0.4806image
ENSG00000253731.2,PCDHGA6MESOGSVA_HALLMARK_FATTY_ACID_METABOLISMEAG3.2542e-02-0.4203image
ENSG00000253731.2,PCDHGA6OVGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEAG1.3566e-020.3224image
chr5:141377328-141378451:+OVGSVA_HALLMARK_KRAS_SIGNALING_DNEER1.5001e-020.4807image
ENSG00000253731.2,PCDHGA6PRADGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG8.9714e-030.3319image
chr5:141377328-141378451:+PRADGSVA_HALLMARK_MITOTIC_SPINDLEEER4.1715e-020.2756image
chr5:141377328-141378451:+SARCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEER4.3730e-02-0.4552image
ENSG00000253731.2,PCDHGA6SARCGSVA_HALLMARK_MYC_TARGETS_V1EAG6.3067e-030.4873image
chr5:141377328-141378451:+SKCMGSVA_HALLMARK_P53_PATHWAYEER9.7082e-030.4312image
ENSG00000253731.2,PCDHGA6SKCMGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEAG1.1891e-040.4765image
ENSG00000253731.2,PCDHGA6STADGSVA_HALLMARK_ADIPOGENESISEAG4.6045e-040.4133image
ENSG00000253731.2,PCDHGA6THCAGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG3.5073e-03-0.2724image
chr5:141377328-141378451:+THYMGSVA_HALLMARK_MYC_TARGETS_V2EER1.6429e-02-0.4276image
ENSG00000253731.2,PCDHGA6THYMGSVA_HALLMARK_APICAL_SURFACEEAG8.8174e-030.3947image


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7. Enriched editing regions and drugs for PCDHGA6


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
ENSG00000253731.2,PCDHGA6BRCACamptothecinEAG3.8843e-02-0.2530image
ENSG00000253731.2,PCDHGA6ESCALFM.A13EAG1.9308e-030.4755image
chr5:141377328-141378451:+KIRCBMS.536924EER4.3316e-04-0.4122image
ENSG00000253731.2,PCDHGA6KIRCBMS.536924EAG1.9857e-03-0.3449image
ENSG00000253731.2,PCDHGA6KIRPEHT.1864EAG2.3541e-020.4124image
chr5:141377328-141378451:+KIRPFH535EER2.8475e-020.4471image
chr5:141377328-141378451:+LUADErlotinibEER5.3386e-03-0.5502image
ENSG00000253731.2,PCDHGA6LUADCCT007093EAG1.2226e-020.4312image
chr5:141377328-141378451:+MESOFH535EER5.9702e-030.5442image
ENSG00000253731.2,PCDHGA6MESOFH535EAG7.9611e-030.5087image
ENSG00000253731.2,PCDHGA6OVA.770041EAG2.1048e-04-0.4682image
chr5:141377328-141378451:+PRADMG.132EER2.9440e-030.3937image
chr5:141377328-141378451:+SARCFH535EER4.8099e-02-0.4471image
ENSG00000253731.2,PCDHGA6SARCBI.D1870EAG3.7157e-02-0.3822image
chr5:141377328-141378451:+SKCMDocetaxelEER3.3145e-020.3610image
ENSG00000253731.2,PCDHGA6SKCMDMOGEAG1.0426e-04-0.4800image
ENSG00000253731.2,PCDHGA6STADMetforminEAG1.4979e-02-0.2939image
ENSG00000253731.2,PCDHGA6TGCTAS601245EAG3.9397e-020.4638image
ENSG00000253731.2,PCDHGA6THCAGefitinibEAG1.1307e-05-0.4001image
chr5:141377328-141378451:+THYMGW.441756EER4.4407e-03-0.4971image
ENSG00000253731.2,PCDHGA6THYMMethotrexateEAG1.7955e-030.4624image


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