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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: PAAF1 (ImmuneEditome ID:80227)

1. Gene summary of enriched editing regions for PAAF1

check button Gene summary
Gene informationGene symbol

PAAF1

Gene ID

80227

GeneSynonymsPAAF|Rpn14|WDR71
GeneCytomap

11q13.4

GeneTypeprotein-coding
GeneDescriptionproteasomal ATPase-associated factor 1|WD repeat domain 71|WD repeat-containing protein 71
GeneModificationdate20230329
UniprotIDQ9BRP4;F5H103;F5H0C4;F5H3E9;F5H3I1;F5H5D4;F5H0F7
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr11:73879553-73881434:+ENST00000381783.4ENSG00000175575.11PAAF1ncRNA_exonic(ATAT)n,AluSx1,AluJo,AluJb,AluYh3,AluJr,AluSq2,(CA)nchr11:73879553-73881434:+.alignment
chr11:73882523-73886624:+ENST00000310571.6ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000504441.5ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000535604.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000536003.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000541951.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000542293.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000543814.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000544552.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73882523-73886624:+ENST00000546039.4ENSG00000175575.11PAAF1intronicL1MB7,L2c,AluY,L2,AluJr,AluJo,FLAM_C,AluSz6,AluSq2,AluSg,AluYa5chr11:73882523-73886624:+.alignment
chr11:73891619-73892251:+ENST00000543079.1ENSG00000175575.11PAAF1ncRNA_intronicAluJr,AluJbchr11:73891619-73892251:+.alignment
chr11:73929098-73930707:+ENST00000535936.1ENSG00000175575.11PAAF1ncRNA_exonicAluY,AluSx1,AluSp,L1MA8,AluJbchr11:73929098-73930707:+.alignment


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2. Tumor-specific enriched editing regions for PAAF1


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
chr11:73929098-73930707:+KIRCEER4.0814e-022.7899e-022.3894e+04image

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3. Enriched editing regions and immune related genes for PAAF1


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 PAAF1


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

More results



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5. Enriched editing regions and immune infiltration for PAAF1


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
chr11:73929098-73930707:+BRCAEERT_cells_CD81.4695e-03-0.3024image
ENSG00000175575.11,PAAF1BRCAEAGDendritic_cells_activated1.2871e-020.2246image
chr11:73879553-73881434:+ESCAEERB_cells_memory4.8498e-030.4653image
ENSG00000175575.11,PAAF1ESCAEAGDendritic_cells_resting2.6595e-02-0.3342image
chr11:73879553-73881434:+GBMEERB_cells_memory4.3514e-030.5058image
chr11:73929098-73930707:+KIRCEERNK_cells_resting3.3171e-020.3558image
ENSG00000175575.11,PAAF1LAMLEAGMast_cells_resting2.0612e-02-0.2889image
chr11:73879553-73881434:+LGGEERMacrophages_M01.5228e-030.2636image
chr11:73882523-73886624:+LGGEERMast_cells_activated3.7191e-02-0.1233image
ENSG00000175575.11,PAAF1LGGEAGMast_cells_activated3.2387e-02-0.1200image
chr11:73879553-73881434:+OVEERT_cells_gamma_delta3.0665e-030.2750image
chr11:73882523-73886624:+OVEERDendritic_cells_activated4.3349e-020.1930image
ENSG00000175575.11,PAAF1SKCMEAGDendritic_cells_resting4.5602e-030.5289image
chr11:73879553-73881434:+STADEERT_cells_regulatory_(Tregs)6.3416e-03-0.3327image
chr11:73882523-73886624:+STADEERMacrophages_M21.5182e-030.4590image
ENSG00000175575.11,PAAF1STADEAGMacrophages_M23.9050e-020.2067image
ENSG00000175575.11,PAAF1THCAEAGMast_cells_resting2.1193e-02-0.3997image


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6. Enriched editing regions and immune gene sets for PAAF1


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
ENSG00000175575.11,PAAF1BRCAGSVA_HALLMARK_UV_RESPONSE_DNEAG5.4793e-040.3084image
chr11:73929098-73930707:+BRCAGSVA_HALLMARK_UV_RESPONSE_DNEER8.3988e-030.2524image
ENSG00000175575.11,PAAF1ESCAGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG1.7283e-020.3572image
chr11:73879553-73881434:+ESCAGSVA_HALLMARK_PANCREAS_BETA_CELLSEER9.5152e-030.4322image
ENSG00000175575.11,PAAF1GBMGSVA_HALLMARK_ADIPOGENESISEAG2.4275e-040.4923image
chr11:73882523-73886624:+GBMGSVA_HALLMARK_ADIPOGENESISEER6.7102e-030.3942image
chr11:73879553-73881434:+GBMGSVA_HALLMARK_GLYCOLYSISEER8.7248e-050.6545image
chr11:73929098-73930707:+KIRCGSVA_HALLMARK_MITOTIC_SPINDLEEER2.1632e-020.3816image
chr11:73882523-73886624:+KIRCGSVA_HALLMARK_HYPOXIAEER4.5104e-020.3887image
ENSG00000175575.11,PAAF1LAMLGSVA_HALLMARK_NOTCH_SIGNALINGEAG4.2372e-030.3529image
chr11:73882523-73886624:+LGGGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEER1.8142e-020.1396image
chr11:73879553-73881434:+LGGGSVA_HALLMARK_SPERMATOGENESISEER2.4217e-020.1891image
ENSG00000175575.11,PAAF1LGGGSVA_HALLMARK_ANDROGEN_RESPONSEEAG1.3862e-030.1786image
ENSG00000175575.11,PAAF1LUADGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEAG9.3253e-030.5298image
chr11:73882523-73886624:+OVGSVA_HALLMARK_UV_RESPONSE_UPEER1.5582e-040.3529image
chr11:73879553-73881434:+OVGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER2.2117e-020.2142image
ENSG00000175575.11,PAAF1OVGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG1.9618e-040.2986image
ENSG00000175575.11,PAAF1SKCMGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG4.0161e-030.5352image
chr11:73882523-73886624:+STADGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER4.2044e-02-0.3044image
chr11:73879553-73881434:+STADGSVA_HALLMARK_P53_PATHWAYEER3.3425e-02-0.2622image
ENSG00000175575.11,PAAF1THCAGSVA_HALLMARK_DNA_REPAIREAG2.5391e-020.3887image
chr11:73929098-73930707:+THCAGSVA_HALLMARK_APICAL_JUNCTIONEER3.7175e-020.3887image


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7. Enriched editing regions and drugs for PAAF1


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
ENSG00000175575.11,PAAF1BRCAEHT.1864EAG3.5150e-040.3184image
chr11:73929098-73930707:+BRCAEHT.1864EER2.3087e-040.3473image
ENSG00000175575.11,PAAF1ESCAAZD6244EAG4.0964e-03-0.4243image
chr11:73879553-73881434:+ESCAAZD6244EER2.0981e-02-0.3888image
ENSG00000175575.11,PAAF1GBMBIRB.0796EAG1.3905e-020.3424image
chr11:73882523-73886624:+GBMCyclopamineEER1.5750e-03-0.4529image
chr11:73879553-73881434:+GBMImatinibEER4.6287e-030.5028image
chr11:73929098-73930707:+KIRCCHIR.99021EER2.0995e-02-0.3834image
chr11:73882523-73886624:+KIRCCytarabineEER2.4861e-020.4308image
ENSG00000175575.11,PAAF1KIRCAZD7762EAG4.5151e-02-0.2369image
ENSG00000175575.11,PAAF1LAMLATRAEAG2.5010e-020.2800image
chr11:73879553-73881434:+LGGGNF.2EER9.3352e-030.2174image
ENSG00000175575.11,PAAF1LGGDMOGEAG1.8093e-02-0.1325image
ENSG00000175575.11,PAAF1LUADCHIR.99021EAG4.6534e-03-0.5684image
chr11:73882523-73886624:+OVAKT.inhibitor.VIIIEER6.6060e-030.2575image
chr11:73879553-73881434:+OVBAY.61.3606EER7.3169e-030.2500image
ENSG00000175575.11,PAAF1OVMG.132EAG1.2496e-04-0.3081image
chr11:73929098-73930707:+OVBryostatin.1EER9.5454e-03-0.3562image
ENSG00000175575.11,PAAF1SKCMAMG.706EAG2.3970e-03-0.5598image
chr11:73882523-73886624:+STADCytarabineEER6.2177e-040.4907image
chr11:73879553-73881434:+STADCytarabineEER3.1748e-02-0.2647image
ENSG00000175575.11,PAAF1STADCI.1040EAG2.0714e-020.2311image
chr11:73929098-73930707:+THCAAxitinibEER1.0323e-020.4687image


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