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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: PDZD7 (ImmuneEditome ID:79955)

1. Gene summary of enriched editing regions for PDZD7

check button Gene summary
Gene informationGene symbol

PDZD7

Gene ID

79955

GeneSynonymsDFNB57|PDZK7
GeneCytomap

10q24.31

GeneTypeprotein-coding
GeneDescriptionPDZ domain-containing protein 7|deafness, autosomal recessive 57
GeneModificationdate20230517
UniprotIDQ9H5P4;A0A2R8Y4R0;A0A2R8Y892;A0A2R8Y6B4;S4R3J9;A0A2R8YFN1
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr10:101017424-101017634:-ENST00000370215.6ENSG00000186862.16PDZD7exonicAluSq2,FLAM_Cchr10:101017424-101017634:-.alignment


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2. Tumor-specific enriched editing regions for PDZD7


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

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3. Enriched editing regions and immune related genes for PDZD7


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
chr10:101017424-101017634:-PCPGEERENSG00000152332,UHMK10.56591.1898e-099.3857e-150.5719imageNNNAT_cells_CD8GSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000160710,ADAR0.54421.1109e-081.4831e-120.5305imageNNADART_cells_CD8GSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000162735,PEX190.53981.4100e-086.7934e-140.5564imageNNNAT_cells_CD4_memory_activatedGSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000159348,CYB5R10.54081.5643e-081.3011e-100.4885imageNNNAB_cells_naiveGSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000182134,TDRKH0.53502.2771e-085.0627e-120.5195imageNNNADendritic_cells_restingGSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000131779,PEX11B0.53113.5713e-082.9778e-120.5243imageNNNAT_cells_CD8GSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000143252,SDHC0.52983.9359e-089.6540e-130.5342imageNNNAGSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000143390,RFX50.52157.2330e-088.2346e-120.5151imageNNRFX5T_cells_CD8GSVA_HALLMARK_SPERMATOGENESIS
chr10:101017424-101017634:-PCPGEERENSG00000236675,MTX1P10.51988.6767e-089.7494e-120.5135imageNNNAGSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-PCPGEERENSG00000143436,MRPL90.51781.0468e-073.8943e-110.5004imageNNNAT_cells_CD8GSVA_HALLMARK_DNA_REPAIR

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4. Enriched editing regions and immune related splicing for PDZD7


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
chr10:101017424-101017634:-
PCPGEERESENSG00000180964.12chrX103253889:103254017:103254604:103254677:103255077:1032551850.48933.7165e-063.2123e-090.4545imageNNNAT_cells_regulatory_(Tregs)GSVA_HALLMARK_PROTEIN_SECRETION
chr10:101017424-101017634:-
PCPGEERIRENSG00000108671.5chr1732480191:32480631:32480752:324809620.38991.4363e-033.7245e-080.4257imageNNPSMD11T_cells_regulatory_(Tregs)GSVA_HALLMARK_BILE_ACID_METABOLISM
chr10:101017424-101017634:-
PCPGEERA5ENSG00000008838.13chr1740033344:40033456:40035116:40035349:40034915:400353490.32802.7246e-032.1528e-060.4253imageNNNAMast_cells_restingGSVA_HALLMARK_BILE_ACID_METABOLISM
chr10:101017424-101017634:-
PCPGEERESENSG00000105429.8chr1942370700:42370831:42371349:42371482:42375506:42375773-0.36131.4781e-033.4177e-07-0.4265imageNNNAB_cells_memoryGSVA_HALLMARK_HYPOXIA
ENSG00000186862.16,PDZD7
PCPGEAGESENSG00000141552.13chr1781891731:81891833:81893551:81893614:81894466:818944830.44286.5521e-051.6548e-080.4355imageNADAR;BUD13;CNBP;CPSF6;CSTF2T;DGCR8;EIF4A3;EIF4G2;FAM120A;FBL;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPM;HNRNPUL1;LIN28;LIN28B;NOP56;NOP58;PCBP2;PRPF8;PTBP1;RBFOX2;SF3B4;SLTM;SRSF1;SRSF7;TAF15;TARDBP;U2AF1;U2AF2;UPF1;ZNF184NAGSVA_HALLMARK_HEME_METABOLISM
ENSG00000186862.16,PDZD7
PCPGEAGA5ENSG00000008838.13chr1740033344:40033456:40035116:40035349:40034915:400353490.33501.6366e-031.2019e-060.4348imageNADAR;BUD13;CNBP;CPSF6;CSTF2T;DGCR8;DKC1;EIF4A3;EIF4G2;FAM120A;FBL;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPM;HNRNPUL1;LIN28;LIN28B;NOP56;NOP58;PCBP2;PRPF8;PTBP1;RBFOX2;SF3B4;SLTM;SRSF1;SRSF7;TAF15;TARDBP;U2AF1;U2AF2;UPF1;ZNF184NAMast_cells_restingGSVA_HALLMARK_BILE_ACID_METABOLISM
ENSG00000186862.16,PDZD7
PCPGEAGIRENSG00000125459.10chr1155613656:155613766:155614061:155614931-0.41282.2357e-042.1717e-07-0.4069imageNADAR;BUD13;CNBP;CSTF2T;EIF4A3;FBL;FUS;HNRNPA2B1;HNRNPK;LIN28;NOP56;NOP58;PCBP2;PRPF8;PTBP1;SF3B4;SRSF1;SRSF7;TAF15;TARDBP;U2AF1;U2AF2;UPF1NADendritic_cells_restingGSVA_HALLMARK_PROTEIN_SECRETION
ENSG00000186862.16,PDZD7
PCPGEAGESENSG00000180964.12chrX103253889:103254017:103254604:103254677:103255077:1032551850.49063.0844e-063.0891e-090.4549imageNBUD13;CNBP;CPSF6;CSTF2T;DGCR8;EIF4A3;EIF4G2;FAM120A;FBL;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPM;HNRNPUL1;LIN28;LIN28B;NOP56;NOP58;PRPF8;PTBP1;RBFOX2;SF3B4;SLTM;SRSF1;SRSF7;TAF15;TARDBP;U2AF2;UPF1;ZNF184NAT_cells_regulatory_(Tregs)GSVA_HALLMARK_PROTEIN_SECRETION
ENSG00000186862.16,PDZD7
PCPGEAGESENSG00000055917.11chr220263192:20263460:20278582:20278819:20282946:20283228-0.27552.8315e-026.7433e-06-0.4110imageNADAR;BUD13;CNBP;CPSF6;CSTF2T;DGCR8;DKC1;EIF4A3;EIF4G2;FAM120A;FBL;FUS;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPM;HNRNPUL1;LIN28;LIN28B;NOP56;NOP58;PCBP2;PRPF8;PTBP1;RBFOX2;SF3B4;SLTM;SRSF1;SRSF7;TAF15;TARDBP;U2AF1;U2AF2;UPF1;ZNF184NAT_cells_CD8GSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE
chr10:101017424-101017634:-
PCPGEERIRENSG00000198131.9chr1958245786:58246427:58246745:58246794-0.33781.5611e-031.6247e-06-0.4184imageNNNAMacrophages_M2GSVA_HALLMARK_PROTEIN_SECRETION

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5. Enriched editing regions and immune infiltration for PDZD7


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
chr10:101017424-101017634:-LGGEERMacrophages_M06.1502e-03-0.2540image
ENSG00000186862.16,PDZD7LGGEAGMacrophages_M03.9588e-03-0.2667image
ENSG00000186862.16,PDZD7LUADEAGMast_cells_activated3.8128e-020.4348image
chr10:101017424-101017634:-PCPGEERMast_cells_resting1.0583e-02-0.2054image
ENSG00000186862.16,PDZD7PCPGEAGMast_cells_resting9.3904e-03-0.2087image
ENSG00000186862.16,PDZD7SKCMEAGMast_cells_activated3.2111e-030.5992image
ENSG00000186862.16,PDZD7STADEAGT_cells_CD4_memory_resting2.6774e-02-0.4339image


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6. Enriched editing regions and immune gene sets for PDZD7


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
ENSG00000186862.16,PDZD7BRCAGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEAG1.8270e-030.4221image
ENSG00000186862.16,PDZD7LUADGSVA_HALLMARK_MYC_TARGETS_V1EAG2.7370e-020.4596image
ENSG00000186862.16,PDZD7OVGSVA_HALLMARK_NOTCH_SIGNALINGEAG3.3795e-04-0.5861image
ENSG00000186862.16,PDZD7PCPGGSVA_HALLMARK_BILE_ACID_METABOLISMEAG7.1796e-080.4175image
chr10:101017424-101017634:-PCPGGSVA_HALLMARK_BILE_ACID_METABOLISMEER5.7707e-080.4202image
ENSG00000186862.16,PDZD7SKCMGSVA_HALLMARK_MYC_TARGETS_V2EAG3.8631e-02-0.4436image
ENSG00000186862.16,PDZD7STADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG1.7803e-020.4609image


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7. Enriched editing regions and drugs for PDZD7


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
ENSG00000186862.16,PDZD7BRCAABT.263EAG1.5543e-030.4279image
chr10:101017424-101017634:-LGGJNK.Inhibitor.VIIIEER2.1838e-02-0.2137image
ENSG00000186862.16,PDZD7LGGJNK.Inhibitor.VIIIEAG2.3028e-02-0.2119image
ENSG00000186862.16,PDZD7LUADEmbelinEAG3.0941e-03-0.5892image
ENSG00000186862.16,PDZD7OVBIBW2992EAG2.3228e-03-0.5120image
ENSG00000186862.16,PDZD7PCPGAZD.2281EAG5.2860e-070.3911image
chr10:101017424-101017634:-PCPGAZD.2281EER5.1736e-070.3914image
ENSG00000186862.16,PDZD7SKCMBIBW2992EAG1.7974e-03-0.6268image
ENSG00000186862.16,PDZD7STADABT.263EAG1.0603e-030.6050image


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