CAeditome Logo

Home

Download

Statistics

Landscape

Help

Contact
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: GDPD1 (ImmuneEditome ID:284161)

1. Gene summary of enriched editing regions for GDPD1

check button Gene summary
Gene informationGene symbol

GDPD1

Gene ID

284161

GeneSynonymsGDE4
GeneCytomap

17q22

GeneTypeprotein-coding
GeneDescriptionlysophospholipase D GDPD1|glycerophosphodiester phosphodiesterase 4|glycerophosphodiester phosphodiesterase domain-containing protein 1
GeneModificationdate20230329
UniprotIDQ8N9F7;J3QQN7;J3QRR6;J3KTA9
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr17:59250460-59251029:+ENST00000284116.7ENSG00000153982.9GDPD1intronicAluJr,AluSx1,MIR3chr17:59250460-59251029:+.alignment
chr17:59250460-59251029:+ENST00000578026.4ENSG00000153982.9GDPD1intronicAluJr,AluSx1,MIR3chr17:59250460-59251029:+.alignment
chr17:59250460-59251029:+ENST00000579020.4ENSG00000153982.9GDPD1intronicAluJr,AluSx1,MIR3chr17:59250460-59251029:+.alignment
chr17:59250460-59251029:+ENST00000581140.4ENSG00000153982.9GDPD1intronicAluJr,AluSx1,MIR3chr17:59250460-59251029:+.alignment
chr17:59250460-59251029:+ENST00000581276.4ENSG00000153982.9GDPD1intronicAluJr,AluSx1,MIR3chr17:59250460-59251029:+.alignment
chr17:59274055-59275165:+ENST00000581140.4ENSG00000153982.9GDPD1exonicAluY,AluSx1,AluSz6chr17:59274055-59275165:+.alignment


Top

2. Tumor-specific enriched editing regions for GDPD1


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


Top

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


Top

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

Top

3. Enriched editing regions and immune related genes for GDPD1


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



Top

4. Enriched editing regions and immune related splicing for GDPD1


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



Top

5. Enriched editing regions and immune infiltration for GDPD1


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
chr17:59274055-59275165:+BLCAEERT_cells_CD4_naive3.4132e-02-0.1666image
ENSG00000153982.9,GDPD1BLCAEAGT_cells_CD4_naive3.8985e-02-0.1619image
chr17:59274055-59275165:+BRCAEERPlasma_cells2.5119e-020.0894image
ENSG00000153982.9,GDPD1BRCAEAGPlasma_cells2.5140e-020.0894image
chr17:59274055-59275165:+CESCEERB_cells_naive1.3910e-020.3109image
ENSG00000153982.9,GDPD1CESCEAGB_cells_naive1.6183e-020.3043image
chr17:59274055-59275165:+COADEERNeutrophils1.3948e-040.4457image
ENSG00000153982.9,GDPD1COADEAGNeutrophils1.3948e-040.4457image
chr17:59274055-59275165:+GBMEERDendritic_cells_resting2.6045e-040.2979image
ENSG00000153982.9,GDPD1GBMEAGDendritic_cells_resting2.6045e-040.2979image
chr17:59274055-59275165:+KIRCEERMacrophages_M13.4263e-020.2610image
ENSG00000153982.9,GDPD1KIRCEAGMacrophages_M13.4263e-020.2610image
chr17:59274055-59275165:+KIRPEERNeutrophils6.5614e-030.2650image
ENSG00000153982.9,GDPD1KIRPEAGNeutrophils6.5614e-030.2650image
chr17:59274055-59275165:+LGGEERMast_cells_resting4.1890e-030.1260image
ENSG00000153982.9,GDPD1LGGEAGMast_cells_resting5.0386e-030.1234image
chr17:59274055-59275165:+LIHCEERNK_cells_resting5.0128e-040.4577image
ENSG00000153982.9,GDPD1LIHCEAGNK_cells_resting4.0011e-020.2778image
chr17:59274055-59275165:+LUADEERT_cells_CD86.1714e-030.1588image
ENSG00000153982.9,GDPD1LUADEAGT_cells_CD86.1714e-030.1588image
chr17:59274055-59275165:+LUSCEERB_cells_memory1.1800e-030.3384image
ENSG00000153982.9,GDPD1LUSCEAGB_cells_memory1.1800e-030.3384image
chr17:59274055-59275165:+PRADEERT_cells_follicular_helper3.1522e-02-0.1073image
ENSG00000153982.9,GDPD1PRADEAGT_cells_follicular_helper3.5583e-02-0.1049image
chr17:59274055-59275165:+SKCMEERMonocytes4.6641e-02-0.1502image
ENSG00000153982.9,GDPD1SKCMEAGMonocytes4.6641e-02-0.1502image
chr17:59274055-59275165:+STADEERT_cells_CD4_memory_activated5.6354e-050.2417image
ENSG00000153982.9,GDPD1STADEAGT_cells_CD4_memory_activated4.8739e-050.2428image
chr17:59274055-59275165:+TGCTEERMacrophages_M22.1689e-02-0.2431image
ENSG00000153982.9,GDPD1TGCTEAGMacrophages_M22.1689e-02-0.2431image
chr17:59274055-59275165:+THCAEERMonocytes2.2069e-02-0.1519image
ENSG00000153982.9,GDPD1THCAEAGMonocytes2.2069e-02-0.1519image
chr17:59274055-59275165:+UCECEERMonocytes1.2594e-020.3152image
ENSG00000153982.9,GDPD1UCECEAGMonocytes1.1797e-020.3154image
ENSG00000153982.9,GDPD1UCSEAGMast_cells_resting1.1255e-020.5185image


Top

6. Enriched editing regions and immune gene sets for GDPD1


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


Top

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


Top

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
ENSG00000153982.9,GDPD1BLCAGSVA_HALLMARK_KRAS_SIGNALING_DNEAG3.1306e-020.1687image
chr17:59274055-59275165:+BLCAGSVA_HALLMARK_KRAS_SIGNALING_DNEER3.7956e-020.1632image
chr17:59274055-59275165:+BRCAGSVA_HALLMARK_KRAS_SIGNALING_DNEER5.2117e-060.1808image
ENSG00000153982.9,GDPD1BRCAGSVA_HALLMARK_KRAS_SIGNALING_DNEAG5.1478e-060.1809image
chr17:59274055-59275165:+CESCGSVA_HALLMARK_ANDROGEN_RESPONSEEER1.1935e-02-0.3174image
ENSG00000153982.9,GDPD1CESCGSVA_HALLMARK_ANDROGEN_RESPONSEEAG9.6602e-03-0.3262image
chr17:59274055-59275165:+COADGSVA_HALLMARK_DNA_REPAIREER8.6647e-04-0.3947image
ENSG00000153982.9,GDPD1COADGSVA_HALLMARK_DNA_REPAIREAG8.6647e-04-0.3947image
chr17:59274055-59275165:+ESCAGSVA_HALLMARK_MYC_TARGETS_V1EER4.4704e-02-0.2295image
ENSG00000153982.9,GDPD1ESCAGSVA_HALLMARK_MYC_TARGETS_V1EAG4.6738e-02-0.2259image
chr17:59274055-59275165:+GBMGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER1.4135e-040.3098image
ENSG00000153982.9,GDPD1GBMGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG1.4135e-040.3098image
chr17:59274055-59275165:+KIRPGSVA_HALLMARK_MYOGENESISEER6.1190e-030.2671image
ENSG00000153982.9,GDPD1KIRPGSVA_HALLMARK_MYOGENESISEAG6.1190e-030.2671image
chr17:59274055-59275165:+LGGGSVA_HALLMARK_ANGIOGENESISEER1.9207e-030.1364image
ENSG00000153982.9,GDPD1LGGGSVA_HALLMARK_ANGIOGENESISEAG1.5224e-030.1394image
ENSG00000153982.9,GDPD1LIHCGSVA_HALLMARK_MITOTIC_SPINDLEEAG1.8667e-02-0.3162image
ENSG00000153982.9,GDPD1LUADGSVA_HALLMARK_NOTCH_SIGNALINGEAG7.8616e-04-0.1941image
chr17:59274055-59275165:+LUADGSVA_HALLMARK_NOTCH_SIGNALINGEER7.8616e-04-0.1941image
chr17:59274055-59275165:+LUSCGSVA_HALLMARK_MTORC1_SIGNALINGEER2.4444e-02-0.2384image
ENSG00000153982.9,GDPD1LUSCGSVA_HALLMARK_MTORC1_SIGNALINGEAG2.4444e-02-0.2384image
chr17:59274055-59275165:+OVGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER2.6943e-020.1682image
ENSG00000153982.9,GDPD1OVGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG2.6943e-020.1682image
chr17:59274055-59275165:+PCPGGSVA_HALLMARK_HEDGEHOG_SIGNALINGEER1.8596e-04-0.3460image
ENSG00000153982.9,GDPD1PCPGGSVA_HALLMARK_HEDGEHOG_SIGNALINGEAG1.8596e-04-0.3460image
ENSG00000153982.9,GDPD1PRADGSVA_HALLMARK_G2M_CHECKPOINTEAG2.7508e-06-0.2314image
chr17:59274055-59275165:+PRADGSVA_HALLMARK_G2M_CHECKPOINTEER4.5910e-06-0.2263image
ENSG00000153982.9,GDPD1READGSVA_HALLMARK_P53_PATHWAYEAG2.0793e-020.5127image
chr17:59274055-59275165:+SKCMGSVA_HALLMARK_KRAS_SIGNALING_DNEER1.7097e-020.1796image
ENSG00000153982.9,GDPD1SKCMGSVA_HALLMARK_KRAS_SIGNALING_DNEAG1.7097e-020.1796image
ENSG00000153982.9,GDPD1STADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG8.1431e-060.2659image
chr17:59274055-59275165:+STADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER1.1005e-050.2631image
ENSG00000153982.9,GDPD1TGCTGSVA_HALLMARK_E2F_TARGETSEAG1.0191e-020.2711image
chr17:59274055-59275165:+TGCTGSVA_HALLMARK_E2F_TARGETSEER1.0191e-020.2711image
ENSG00000153982.9,GDPD1THCAGSVA_HALLMARK_HEME_METABOLISMEAG3.4085e-04-0.2357image
chr17:59274055-59275165:+THCAGSVA_HALLMARK_HEME_METABOLISMEER3.4085e-04-0.2357image
chr17:59274055-59275165:+UCECGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER1.7630e-03-0.3893image
ENSG00000153982.9,GDPD1UCECGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG1.5327e-03-0.3910image
ENSG00000153982.9,GDPD1UCSGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG1.7202e-020.4916image


Top

7. Enriched editing regions and drugs for GDPD1


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
ENSG00000153982.9,GDPD1BLCAGSK.650394EAG6.3738e-030.2128image
chr17:59274055-59275165:+BLCAKIN001.135EER7.3502e-03-0.2099image
ENSG00000153982.9,GDPD1BRCAMG.132EAG6.6400e-09-0.2294image
chr17:59274055-59275165:+BRCAMG.132EER7.1098e-09-0.2289image
chr17:59274055-59275165:+CESCErlotinibEER3.3520e-02-0.2704image
ENSG00000153982.9,GDPD1CESCErlotinibEAG2.2029e-02-0.2904image
ENSG00000153982.9,GDPD1COADGW843682XEAG3.7361e-060.5278image
chr17:59274055-59275165:+COADGW843682XEER3.7361e-060.5278image
chr17:59274055-59275165:+ESCAA.770041EER2.2596e-020.2596image
ENSG00000153982.9,GDPD1ESCAA.770041EAG2.6337e-020.2515image
chr17:59274055-59275165:+GBMBIBW2992EER7.9889e-04-0.2745image
ENSG00000153982.9,GDPD1GBMBIBW2992EAG7.9889e-04-0.2745image
chr17:59274055-59275165:+LGGCMKEER3.7060e-04-0.1563image
ENSG00000153982.9,GDPD1LGGCMKEAG8.7016e-04-0.1463image
ENSG00000153982.9,GDPD1LIHCGNF.2EAG2.1187e-05-0.5397image
chr17:59274055-59275165:+LIHCAMG.706EER1.0868e-03-0.4326image
ENSG00000153982.9,GDPD1LUADAZD6244EAG4.7770e-03-0.1636image
chr17:59274055-59275165:+LUADAZD6244EER4.7770e-03-0.1636image
chr17:59274055-59275165:+LUSCCGP.082996EER4.5386e-020.2127image
ENSG00000153982.9,GDPD1LUSCCGP.082996EAG4.5386e-020.2127image
ENSG00000153982.9,GDPD1OVCMKEAG2.5201e-02-0.1702image
chr17:59274055-59275165:+OVCMKEER2.5201e-02-0.1702image
ENSG00000153982.9,GDPD1PRADIPA.3EAG2.3041e-050.2094image
chr17:59274055-59275165:+PRADIPA.3EER2.6699e-050.2078image
ENSG00000153982.9,GDPD1READGSK.650394EAG3.6980e-02-0.4690image
chr17:59274055-59275165:+SKCMBMS.536924EER9.0207e-03-0.1974image
ENSG00000153982.9,GDPD1SKCMBMS.536924EAG9.0207e-03-0.1974image
ENSG00000153982.9,GDPD1STADGemcitabineEAG1.6340e-03-0.1894image
chr17:59274055-59275165:+STADGemcitabineEER1.9986e-03-0.1866image
ENSG00000153982.9,GDPD1TGCTKIN001.135EAG9.0090e-030.2754image
chr17:59274055-59275165:+TGCTKIN001.135EER9.0090e-030.2754image
chr17:59274055-59275165:+THCAGDC.0449EER1.8411e-04-0.2458image
ENSG00000153982.9,GDPD1THCAGDC.0449EAG1.8411e-04-0.2458image
ENSG00000153982.9,GDPD1UCECFTI.277EAG4.7360e-020.2509image


Top

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