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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: RABEPK (ImmuneEditome ID:10244)

1. Gene summary of enriched editing regions for RABEPK

check button Gene summary
Gene informationGene symbol

RABEPK

Gene ID

10244

GeneSynonymsRAB9P40|bA65N13.1|p40
GeneCytomap

9q33.3

GeneTypeprotein-coding
GeneDescriptionrab9 effector protein with kelch motifs|40 kDa Rab9 effector protein|Rab9 effector p40
GeneModificationdate20230329
UniprotIDQ7Z6M1;A0A024R8A0;A0A0S2Z4Z5;Q5T1S4;Q5T1S5
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr9:125204277-125205664:+ENST00000259460.11ENSG00000136933.15RABEPKintronicAluJo,AluSz6,AluSc,MIRc,AluY,L2cchr9:125204277-125205664:+.alignment
chr9:125204277-125205664:+ENST00000373538.6ENSG00000136933.15RABEPKintronicAluJo,AluSz6,AluSc,MIRc,AluY,L2cchr9:125204277-125205664:+.alignment
chr9:125204277-125205664:+ENST00000373544.4ENSG00000136933.15RABEPKintronicAluJo,AluSz6,AluSc,MIRc,AluY,L2cchr9:125204277-125205664:+.alignment
chr9:125204277-125205664:+ENST00000394125.7ENSG00000136933.15RABEPKintronicAluJo,AluSz6,AluSc,MIRc,AluY,L2cchr9:125204277-125205664:+.alignment
chr9:125204277-125205664:+ENST00000416065.1ENSG00000136933.15RABEPKintronicAluJo,AluSz6,AluSc,MIRc,AluY,L2cchr9:125204277-125205664:+.alignment
chr9:125204277-125205664:+ENST00000628863.1ENSG00000136933.15RABEPKintronicAluJo,AluSz6,AluSc,MIRc,AluY,L2cchr9:125204277-125205664:+.alignment
chr9:125207931-125208795:+ENST00000259460.11ENSG00000136933.15RABEPKintronicAluSx3,AluSp,AluSx1chr9:125207931-125208795:+.alignment
chr9:125207931-125208795:+ENST00000373538.6ENSG00000136933.15RABEPKintronicAluSx3,AluSp,AluSx1chr9:125207931-125208795:+.alignment
chr9:125207931-125208795:+ENST00000373544.4ENSG00000136933.15RABEPKintronicAluSx3,AluSp,AluSx1chr9:125207931-125208795:+.alignment
chr9:125207931-125208795:+ENST00000394125.7ENSG00000136933.15RABEPKintronicAluSx3,AluSp,AluSx1chr9:125207931-125208795:+.alignment
chr9:125207931-125208795:+ENST00000416065.1ENSG00000136933.15RABEPKintronicAluSx3,AluSp,AluSx1chr9:125207931-125208795:+.alignment
chr9:125207931-125208795:+ENST00000628863.1ENSG00000136933.15RABEPKintronicAluSx3,AluSp,AluSx1chr9:125207931-125208795:+.alignment
chr9:125211246-125214019:+ENST00000373538.6ENSG00000136933.15RABEPKexonicAluSz,Charlie8,(TACA)n,MIRb,AluY,AluSx1,MLT1O,AluYm1,MIR3,AluSc8chr9:125211246-125214019:+.alignment
chr9:125211246-125214019:+ENST00000373544.4ENSG00000136933.15RABEPKexonicAluSz,Charlie8,(TACA)n,MIRb,AluY,AluSx1,MLT1O,AluYm1,MIR3,AluSc8chr9:125211246-125214019:+.alignment
chr9:125211246-125214019:+ENST00000394125.7ENSG00000136933.15RABEPKexonicAluSz,Charlie8,(TACA)n,MIRb,AluY,AluSx1,MLT1O,AluYm1,MIR3,AluSc8chr9:125211246-125214019:+.alignment
chr9:125211246-125214019:+ENST00000416065.1ENSG00000136933.15RABEPKexonicAluSz,Charlie8,(TACA)n,MIRb,AluY,AluSx1,MLT1O,AluYm1,MIR3,AluSc8chr9:125211246-125214019:+.alignment
chr9:125211246-125214019:+ENST00000628863.1ENSG00000136933.15RABEPKexonicAluSz,Charlie8,(TACA)n,MIRb,AluY,AluSx1,MLT1O,AluYm1,MIR3,AluSc8chr9:125211246-125214019:+.alignment
chr9:125216771-125223276:+ENST00000259460.11ENSG00000136933.15RABEPKexonic(ATGTGT)n,AluSg4,AluSz,AluSz6,(TC)n,AluSx3,AluSx,AluJo,AluJb,AluJr,AluSx1,AluY,MIRb,MIR,L1ME4a,A-rich,(AAAT)nchr9:125216771-125223276:+.alignment
chr9:125216771-125223276:+ENST00000373538.6ENSG00000136933.15RABEPKexonic(ATGTGT)n,AluSg4,AluSz,AluSz6,(TC)n,AluSx3,AluSx,AluJo,AluJb,AluJr,AluSx1,AluY,MIRb,MIR,L1ME4a,A-rich,(AAAT)nchr9:125216771-125223276:+.alignment
chr9:125216771-125223276:+ENST00000373544.4ENSG00000136933.15RABEPKexonic(ATGTGT)n,AluSg4,AluSz,AluSz6,(TC)n,AluSx3,AluSx,AluJo,AluJb,AluJr,AluSx1,AluY,MIRb,MIR,L1ME4a,A-rich,(AAAT)nchr9:125216771-125223276:+.alignment
chr9:125216771-125223276:+ENST00000394125.7ENSG00000136933.15RABEPKexonic(ATGTGT)n,AluSg4,AluSz,AluSz6,(TC)n,AluSx3,AluSx,AluJo,AluJb,AluJr,AluSx1,AluY,MIRb,MIR,L1ME4a,A-rich,(AAAT)nchr9:125216771-125223276:+.alignment
chr9:125216771-125223276:+ENST00000416065.1ENSG00000136933.15RABEPKexonic(ATGTGT)n,AluSg4,AluSz,AluSz6,(TC)n,AluSx3,AluSx,AluJo,AluJb,AluJr,AluSx1,AluY,MIRb,MIR,L1ME4a,A-rich,(AAAT)nchr9:125216771-125223276:+.alignment
chr9:125216771-125223276:+ENST00000628863.1ENSG00000136933.15RABEPKexonic(ATGTGT)n,AluSg4,AluSz,AluSz6,(TC)n,AluSx3,AluSx,AluJo,AluJb,AluJr,AluSx1,AluY,MIRb,MIR,L1ME4a,A-rich,(AAAT)nchr9:125216771-125223276:+.alignment


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2. Tumor-specific enriched editing regions for RABEPK


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 RABEPK


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 RABEPK


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 RABEPK


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
chr9:125216771-125223276:+BRCAEERPlasma_cells4.0115e-020.2553image
chr9:125211246-125214019:+ESCAEERT_cells_gamma_delta1.7004e-020.3754image
chr9:125216771-125223276:+ESCAEERMacrophages_M03.8835e-020.2720image
ENSG00000136933.15,RABEPKESCAEAGT_cells_gamma_delta4.9398e-020.2114image
chr9:125216771-125223276:+LIHCEERMacrophages_M12.6733e-050.7962image
ENSG00000136933.15,RABEPKLIHCEAGMacrophages_M12.6733e-050.7962image
chr9:125216771-125223276:+OVEERT_cells_CD4_memory_resting1.1434e-030.3271image
ENSG00000136933.15,RABEPKOVEAGT_cells_CD4_memory_resting2.6480e-030.2918image
chr9:125216771-125223276:+PRADEERDendritic_cells_activated1.3111e-020.5442image
ENSG00000136933.15,RABEPKPRADEAGDendritic_cells_activated1.3111e-020.5442image
chr9:125207931-125208795:+STADEERT_cells_CD4_memory_activated2.3805e-020.2940image


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6. Enriched editing regions and immune gene sets for RABEPK


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
chr9:125216771-125223276:+BRCAGSVA_HALLMARK_HEDGEHOG_SIGNALINGEER1.7947e-030.3800image
ENSG00000136933.15,RABEPKBRCAGSVA_HALLMARK_HEDGEHOG_SIGNALINGEAG5.2108e-050.4640image
chr9:125216771-125223276:+ESCAGSVA_HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITIONEER6.5814e-030.3529image
ENSG00000136933.15,RABEPKLAMLGSVA_HALLMARK_SPERMATOGENESISEAG4.9345e-02-0.2915image
chr9:125216771-125223276:+LIHCGSVA_HALLMARK_HEME_METABOLISMEER1.6915e-020.5272image
ENSG00000136933.15,RABEPKLIHCGSVA_HALLMARK_HEME_METABOLISMEAG1.6915e-020.5272image
ENSG00000136933.15,RABEPKPCPGGSVA_HALLMARK_UV_RESPONSE_DNEAG1.1767e-020.3898image
chr9:125216771-125223276:+PCPGGSVA_HALLMARK_UV_RESPONSE_DNEER1.1767e-020.3898image
chr9:125216771-125223276:+PRADGSVA_HALLMARK_HEDGEHOG_SIGNALINGEER4.0822e-020.4609image
ENSG00000136933.15,RABEPKPRADGSVA_HALLMARK_HEDGEHOG_SIGNALINGEAG4.0822e-020.4609image
ENSG00000136933.15,RABEPKSKCMGSVA_HALLMARK_MYC_TARGETS_V2EAG2.8871e-030.5814image
chr9:125216771-125223276:+SKCMGSVA_HALLMARK_MYC_TARGETS_V2EER9.7418e-030.5272image
chr9:125216771-125223276:+STADGSVA_HALLMARK_HEME_METABOLISMEER2.4098e-040.3759image
chr9:125207931-125208795:+STADGSVA_HALLMARK_PEROXISOMEEER5.6761e-040.4354image
ENSG00000136933.15,RABEPKSTADGSVA_HALLMARK_PEROXISOMEEAG2.7925e-040.3058image
chr9:125211246-125214019:+STADGSVA_HALLMARK_APICAL_SURFACEEER2.2513e-050.5563image


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7. Enriched editing regions and drugs for RABEPK


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
chr9:125216771-125223276:+BRCAEpothilone.BEER3.0009e-020.2694image
ENSG00000136933.15,RABEPKBRCAAZD.0530EAG3.1555e-02-0.2573image
chr9:125216771-125223276:+ESCAKU.55933EER6.3417e-03-0.3544image
chr9:125207931-125208795:+ESCAGW.441756EER9.4442e-03-0.4817image
ENSG00000136933.15,RABEPKESCACMKEAG2.3947e-02-0.2420image
chr9:125216771-125223276:+LIHCKIN001.135EER1.5344e-02-0.5338image
ENSG00000136933.15,RABEPKLIHCKIN001.135EAG1.5344e-02-0.5338image
chr9:125216771-125223276:+OVA.443654EER3.4047e-02-0.2166image
ENSG00000136933.15,RABEPKPCPGAMG.706EAG2.0806e-020.3599image
chr9:125216771-125223276:+PCPGAMG.706EER2.0806e-020.3599image
chr9:125216771-125223276:+PRADAKT.inhibitor.VIIIEER1.6240e-020.5300image
ENSG00000136933.15,RABEPKPRADAKT.inhibitor.VIIIEAG1.6240e-020.5300image
ENSG00000136933.15,RABEPKSKCMAS601245EAG2.0887e-020.4687image
chr9:125216771-125223276:+SKCMBMS.754807EER3.9779e-020.4315image
chr9:125216771-125223276:+STADBleomycinEER1.5087e-020.2541image
chr9:125207931-125208795:+STADAKT.inhibitor.VIIIEER2.8608e-03-0.3816image
ENSG00000136933.15,RABEPKSTADAZD7762EAG1.1614e-02-0.2150image
chr9:125211246-125214019:+STADAZD7762EER1.3996e-03-0.4356image


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