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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: PARVB (ImmuneEditome ID:29780)

1. Gene summary of enriched editing regions for PARVB

check button Gene summary
Gene informationGene symbol

PARVB

Gene ID

29780

GeneSynonymsCGI-56
GeneCytomap

22q13.31

GeneTypeprotein-coding
GeneDescriptionbeta-parvin|affixin
GeneModificationdate20230329
UniprotIDQ9HBI1;A0A087WZB5;B0QYP8
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr22:44096864-44097973:+ENST00000402876.3ENSG00000188677.13PARVBncRNA_intronicMER5Achr22:44096864-44097973:+.alignment
chr22:44096864-44097973:+ENST00000477795.1ENSG00000188677.13PARVBncRNA_intronicMER5Achr22:44096864-44097973:+.alignment
chr22:44169783-44171479:+ENST00000338758.10ENSG00000188677.13PARVBUTR3AluSc,AluJb,AluSz,MLT1Bchr22:44169783-44171479:+.alignment


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2. Tumor-specific enriched editing regions for PARVB


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
ENSG00000188677.13,PARVBUVMPathEAG9.5976e-039.1927e-030.2950image


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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 PARVB


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
chr22:44169783-44171479:+UVMEERENSG00000110925,CSRNP2-0.53536.4634e-041.2019e-05-0.4908imageNDKC1;FUS;IGF2BP2CSRNP2T_cells_follicular_helperGSVA_HALLMARK_PROTEIN_SECRETION
chr22:44169783-44171479:+UVMEERENSG00000172889,EGFL70.52768.0904e-048.0422e-060.4992imageNFUS;IGF2BP2NAGSVA_HALLMARK_APICAL_JUNCTION
chr22:44169783-44171479:+UVMEERENSG00000163349,HIPK1-0.52489.0075e-043.0002e-06-0.5190imageNDKC1;FUS;IGF2BP2HIPK1T_cells_follicular_helperGSVA_HALLMARK_PROTEIN_SECRETION
chr22:44169783-44171479:+UVMEERENSG00000248126,CTD-2012J19.2-0.51749.9247e-048.4236e-05-0.4466imageNNNAGSVA_HALLMARK_KRAS_SIGNALING_DN
chr22:44169783-44171479:+UVMEERENSG00000257093,KIAA1147-0.52209.9664e-043.1636e-05-0.4696imageNDKC1;FUS;IGF2BP2NAGSVA_HALLMARK_MYC_TARGETS_V2
chr22:44169783-44171479:+UVMEERENSG00000180979,LRRC57-0.51981.1159e-036.0944e-06-0.5049imageNDKC1;FUS;IGF2BP2NAT_cells_follicular_helperGSVA_HALLMARK_PROTEIN_SECRETION
chr22:44169783-44171479:+UVMEERENSG00000256235,SMIM3-0.51381.1491e-038.0530e-05-0.4477imageNDKC1;FUS;IGF2BP2NAT_cells_regulatory_(Tregs)GSVA_HALLMARK_KRAS_SIGNALING_UP
chr22:44169783-44171479:+UVMEERENSG00000168283,BMI1-0.49631.6676e-038.0213e-05-0.4478imageNDKC1;FUS;IGF2BP2NAEosinophilsGSVA_HALLMARK_MYOGENESIS
chr22:44169783-44171479:+UVMEERENSG00000132669,RIN2-0.49281.6713e-034.9552e-05-0.4592imageNDKC1;FUS;IGF2BP2RIN2Plasma_cellsGSVA_HALLMARK_PROTEIN_SECRETION
chr22:44169783-44171479:+UVMEERENSG00000137955,RABGGTB-0.50441.6971e-031.0832e-04-0.4404imageNDKC1;FUS;IGF2BP2NAT_cells_follicular_helperGSVA_HALLMARK_MYOGENESIS

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4. Enriched editing regions and immune related splicing for PARVB


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
chr22:44169783-44171479:+
UVMEERESENSG00000197713.10chr2210002656:210002783:210009656:210009736:210015972:2100161120.38722.6955e-027.5378e-040.4167imageNDKC1;FUS;IGF2BP2NAT_cells_regulatory_(Tregs)GSVA_HALLMARK_FATTY_ACID_METABOLISM
chr22:44169783-44171479:+
UVMEERA5ENSG00000140326.8chr1542726309:42726417:42727667:42727769:42727620:42727769-0.42474.0173e-021.8123e-04-0.4330imageNDKC1;FUS;IGF2BP2NAMacrophages_M2GSVA_HALLMARK_KRAS_SIGNALING_DN
chr22:44169783-44171479:+
UVMEERA5ENSG00000002933.3chr7150801535:150801724:150800542:150800828:150800542:1508009680.43221.7525e-021.9017e-040.4710imageNDKC1;FUSNAMonocytesGSVA_HALLMARK_UV_RESPONSE_DN
chr22:44169783-44171479:+
UVMEERIRENSG00000116957.8chr1235448348:235448440:235448669:235448899-0.45523.3597e-025.4298e-05-0.4630imageNNNAT_cells_follicular_helperGSVA_HALLMARK_PROTEIN_SECRETION
chr22:44169783-44171479:+
UVMEERIRENSG00000148803.7chr10133355153:133355505:133355737:133355811-0.40534.2921e-023.4833e-04-0.4398imageNFUSNANK_cells_restingGSVA_HALLMARK_MYOGENESIS
chr22:44169783-44171479:+
UVMEERIRENSG00000197858.6chr8144084721:144085479:144085557:144085743-0.43033.1797e-025.9147e-05-0.4769imageNFUS;IGF2BP2NAT_cells_CD4_memory_restingGSVA_HALLMARK_MYOGENESIS
chr22:44169783-44171479:+
UVMEERMEXENSG00000148180.12chr9121281510:121281562:121286601:121286761:121300064:121300126:121301962:121302149-0.34954.5804e-029.0003e-04-0.4176imageNDKC1;FUS;IGF2BP2GSNGSVA_HALLMARK_ANGIOGENESIS
chr22:44169783-44171479:+
UVMEERIRENSG00000141959.12chr2144319350:44319415:44320086:44320147-0.35584.6745e-023.3274e-04-0.4624imageNDKC1;FUS;IGF2BP2NAGSVA_HALLMARK_MYOGENESIS

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5. Enriched editing regions and immune infiltration for PARVB


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
ENSG00000188677.13,PARVBBLCAEAGMacrophages_M01.4588e-03-0.6018image
ENSG00000188677.13,PARVBBRCAEAGT_cells_regulatory_(Tregs)2.9530e-020.1685image
ENSG00000188677.13,PARVBCOADEAGNeutrophils2.3112e-040.6724image
chr22:44169783-44171479:+ESCAEERT_cells_regulatory_(Tregs)2.8382e-020.2621image
chr22:44169783-44171479:+GBMEERT_cells_gamma_delta1.0511e-020.4212image
ENSG00000188677.13,PARVBGBMEAGDendritic_cells_activated2.2817e-040.5128image
ENSG00000188677.13,PARVBHNSCEAGNK_cells_resting2.8106e-020.2860image
chr22:44169783-44171479:+KIRCEERPlasma_cells1.4848e-020.2519image
ENSG00000188677.13,PARVBKIRCEAGMast_cells_activated1.6571e-02-0.1814image
ENSG00000188677.13,PARVBKIRPEAGMacrophages_M22.0552e-020.4280image
ENSG00000188677.13,PARVBLAMLEAGMacrophages_M28.7897e-030.3110image
ENSG00000188677.13,PARVBLGGEAGMacrophages_M22.0904e-02-0.2285image
ENSG00000188677.13,PARVBLIHCEAGB_cells_naive1.0889e-02-0.4657image
chr22:44169783-44171479:+LUSCEEREosinophils1.3656e-030.5495image
ENSG00000188677.13,PARVBLUSCEAGMast_cells_activated3.0714e-050.4926image
chr22:44169783-44171479:+PCPGEERB_cells_naive4.0397e-020.3533image
ENSG00000188677.13,PARVBPCPGEAGB_cells_naive8.3608e-040.3730image
chr22:44169783-44171479:+PRADEERNK_cells_resting9.9313e-030.3764image
ENSG00000188677.13,PARVBPRADEAGEosinophils1.0076e-020.2501image
ENSG00000188677.13,PARVBSARCEAGNeutrophils3.3295e-020.2234image
chr22:44169783-44171479:+SKCMEERB_cells_naive3.3988e-020.1130image
chr22:44169783-44171479:+STADEERNeutrophils3.4758e-040.2950image
ENSG00000188677.13,PARVBSTADEAGMacrophages_M16.6773e-030.2130image
ENSG00000188677.13,PARVBTHCAEAGT_cells_CD81.8611e-040.2196image
ENSG00000188677.13,PARVBTHYMEAGMacrophages_M12.1338e-020.3934image
chr22:44169783-44171479:+UVMEERT_cells_follicular_helper2.7289e-02-0.2602image
ENSG00000188677.13,PARVBUVMEAGMast_cells_activated1.8556e-02-0.2660image


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6. Enriched editing regions and immune gene sets for PARVB


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
ENSG00000188677.13,PARVBBLCAGSVA_HALLMARK_G2M_CHECKPOINTEAG2.5087e-04-0.6697image
ENSG00000188677.13,PARVBBRCAGSVA_HALLMARK_PEROXISOMEEAG2.3994e-030.2334image
ENSG00000188677.13,PARVBCOADGSVA_HALLMARK_UV_RESPONSE_UPEAG9.9384e-03-0.5055image
ENSG00000188677.13,PARVBHNSCGSVA_HALLMARK_MYOGENESISEAG2.1999e-02-0.2977image
ENSG00000188677.13,PARVBKICHGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG1.0912e-03-0.4181image
ENSG00000188677.13,PARVBKIRCGSVA_HALLMARK_KRAS_SIGNALING_DNEAG3.6600e-020.1586image
chr22:44169783-44171479:+KIRCGSVA_HALLMARK_IL2_STAT5_SIGNALINGEER1.5383e-030.3239image
ENSG00000188677.13,PARVBLAMLGSVA_HALLMARK_HEME_METABOLISMEAG4.4156e-02-0.2413image
chr22:44169783-44171479:+LGGGSVA_HALLMARK_MYOGENESISEER2.4646e-02-0.2744image
ENSG00000188677.13,PARVBLGGGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG1.1543e-02-0.2492image
ENSG00000188677.13,PARVBLIHCGSVA_HALLMARK_COAGULATIONEAG4.1300e-02-0.3812image
ENSG00000188677.13,PARVBLUADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG8.4206e-040.5013image
chr22:44169783-44171479:+LUSCGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER2.4981e-02-0.4020image
ENSG00000188677.13,PARVBOVGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG3.2425e-040.4522image
ENSG00000188677.13,PARVBPAADGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEAG4.2542e-030.5069image
chr22:44169783-44171479:+PRADGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER2.1559e-02-0.3381image
ENSG00000188677.13,PARVBSARCGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG2.7238e-02-0.2315image
chr22:44169783-44171479:+SARCGSVA_HALLMARK_APICAL_SURFACEEER1.3796e-020.3607image
chr22:44169783-44171479:+SKCMGSVA_HALLMARK_UV_RESPONSE_DNEER2.1936e-02-0.1221image
ENSG00000188677.13,PARVBSKCMGSVA_HALLMARK_UV_RESPONSE_DNEAG2.4091e-02-0.1108image
ENSG00000188677.13,PARVBSTADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG1.0376e-020.2015image
chr22:44169783-44171479:+STADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER3.1875e-020.1796image
ENSG00000188677.13,PARVBTHCAGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG3.3126e-040.2112image
ENSG00000188677.13,PARVBTHYMGSVA_HALLMARK_DNA_REPAIREAG4.0302e-02-0.3535image
chr22:44169783-44171479:+UVMGSVA_HALLMARK_ANDROGEN_RESPONSEEER2.6834e-02-0.2609image


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7. Enriched editing regions and drugs for PARVB


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
ENSG00000188677.13,PARVBBLCADoxorubicinEAG2.3231e-040.6723image
ENSG00000188677.13,PARVBBRCACytarabineEAG4.9082e-020.1525image
ENSG00000188677.13,PARVBCOADGW843682XEAG5.7196e-040.6399image
ENSG00000188677.13,PARVBGBMAZD8055EAG3.3640e-02-0.3105image
chr22:44169783-44171479:+GBMCamptothecinEER4.8004e-03-0.4596image
chr22:44169783-44171479:+HNSCDocetaxelEER1.1657e-02-0.4472image
ENSG00000188677.13,PARVBHNSCGW.441756EAG5.4084e-03-0.3577image
chr22:44169783-44171479:+KICHLenalidomideEER6.3921e-04-0.4352image
ENSG00000188677.13,PARVBKICHGefitinibEAG5.8563e-05-0.5024image
chr22:44169783-44171479:+KIRCA.770041EER3.8335e-03-0.2971image
ENSG00000188677.13,PARVBKIRPBMS.536924EAG3.0943e-03-0.5479image
ENSG00000188677.13,PARVBLAMLAICAREAG2.1154e-030.3614image
chr22:44169783-44171479:+LGGBAY.61.3606EER1.9548e-02-0.2847image
ENSG00000188677.13,PARVBLGGMetforminEAG3.7460e-030.2846image
ENSG00000188677.13,PARVBLIHCGDC0941EAG1.5512e-020.4452image
ENSG00000188677.13,PARVBLUADAP.24534EAG6.2253e-030.4202image
ENSG00000188677.13,PARVBLUSCLapatinibEAG1.6281e-02-0.2970image
ENSG00000188677.13,PARVBOVElesclomolEAG8.7046e-030.3386image
chr22:44169783-44171479:+PCPGCI.1040EER4.5661e-030.4746image
ENSG00000188677.13,PARVBPCPGAZD6244EAG4.9273e-020.2249image
ENSG00000188677.13,PARVBPRADCamptothecinEAG1.3063e-020.2415image
chr22:44169783-44171479:+PRADBIBW2992EER1.7533e-02-0.3488image
ENSG00000188677.13,PARVBSARCBAY.61.3606EAG3.3763e-050.4202image
chr22:44169783-44171479:+SARCBicalutamideEER4.7084e-03-0.4095image
chr22:44169783-44171479:+SKCMBMS.708163EER8.4331e-030.1402image
ENSG00000188677.13,PARVBSKCMBortezomibEAG2.0203e-04-0.1817image
ENSG00000188677.13,PARVBSTADAUY922EAG1.0042e-02-0.2024image
chr22:44169783-44171479:+STADEtoposideEER2.3745e-02-0.1890image
ENSG00000188677.13,PARVBTHCAImatinibEAG2.7212e-060.2737image
ENSG00000188677.13,PARVBTHYMKIN001.135EAG3.1206e-03-0.4920image
chr22:44169783-44171479:+UVMGNF.2EER8.2638e-04-0.3855image


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