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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: SNRPD1 (ImmuneEditome ID:6632)

1. Gene summary of enriched editing regions for SNRPD1

check button Gene summary
Gene informationGene symbol

SNRPD1

Gene ID

6632

GeneSynonymsHsT2456|SMD1|SNRPD|Sm-D1
GeneCytomap

18q11.2

GeneTypeprotein-coding
GeneDescriptionsmall nuclear ribonucleoprotein Sm D1|Sm-D autoantigen|small nuclear ribonucleoprotein D1 polypeptide 16kDa pseudogene|snRNP core protein D1
GeneModificationdate20230409
UniprotIDP62314;J3QLI9;J3QLR7
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr18:21630458-21633160:+ENST00000577906.1ENSG00000167088.9SNRPD1ncRNA_exonicAluSg4,(AT)n,LTR33,(T)n,AluSz6,AluJo,AluSx1,AluYchr18:21630458-21633160:+.alignment


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2. Tumor-specific enriched editing regions for SNRPD1


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 SNRPD1


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
chr18:21630458-21633160:+GBMEERENSG00000132274,TRIM220.35624.5675e-031.3489e-060.4151imageNCELF2;EIF4A3;FBL;FUS;HNRNPA1;IGF2BP2;NOP56;RBFOX2;TAF15;TARDBP;U2AF2;UPF1TRIM22Macrophages_M1GSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE
chr18:21630458-21633160:+GBMEERENSG00000010030,ETV70.34646.5062e-033.4045e-060.4003imageNEIF4A3;FBL;FUS;IGF2BP2;RBFOX2;TAF15;TARDBP;U2AF2;UPF1NAMacrophages_M1GSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE
chr18:21630458-21633160:+GBMEERENSG00000100342,APOL10.32321.3748e-024.3462e-100.5201imageNEIF4A3;FBL;FUS;HNRNPA1;HNRNPC;HNRNPK;IGF2BP2;RBFOX2;TAF15;TARDBP;U2AF2;UPF1NAMacrophages_M1GSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE
chr18:21630458-21633160:+GBMEERENSG00000108679,LGALS3BP0.29023.1956e-022.1136e-060.4080imageNEIF4A3;FBL;FUS;HNRNPA1;HNRNPC;HNRNPK;HNRNPM;IGF2BP2;NOP56;RANGAP1;RBFOX2;TAF15;TARDBP;U2AF2;UPF1LGALS3BPMacrophages_M1GSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE

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4. Enriched editing regions and immune related splicing for SNRPD1


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

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5. Enriched editing regions and immune infiltration for SNRPD1


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
chr18:21630458-21633160:+BLCAEERMacrophages_M13.3660e-030.3411image
ENSG00000167088.9,SNRPD1BLCAEAGMacrophages_M13.5503e-030.3393image
ENSG00000167088.9,SNRPD1CESCEAGT_cells_CD4_memory_activated2.1056e-020.2529image
chr18:21630458-21633160:+COADEERDendritic_cells_activated6.8156e-030.3325image
ENSG00000167088.9,SNRPD1COADEAGDendritic_cells_activated8.8677e-030.3198image
chr18:21630458-21633160:+HNSCEEREosinophils7.9406e-040.3768image
ENSG00000167088.9,SNRPD1HNSCEAGEosinophils7.9406e-040.3768image
ENSG00000167088.9,SNRPD1KICHEAGMonocytes2.2914e-020.4624image
chr18:21630458-21633160:+KIRCEEREosinophils3.2871e-030.2941image
ENSG00000167088.9,SNRPD1KIRCEAGEosinophils5.4132e-030.2762image
chr18:21630458-21633160:+KIRPEEREosinophils1.6168e-030.5973image
ENSG00000167088.9,SNRPD1KIRPEAGEosinophils1.6168e-030.5973image
ENSG00000167088.9,SNRPD1LIHCEAGT_cells_regulatory_(Tregs)2.8479e-020.4669image
chr18:21630458-21633160:+LUADEERT_cells_CD87.7627e-040.3480image
ENSG00000167088.9,SNRPD1LUADEAGT_cells_CD87.7627e-040.3480image
ENSG00000167088.9,SNRPD1OVEAGMast_cells_resting4.0166e-02-0.2056image
chr18:21630458-21633160:+PCPGEERDendritic_cells_resting3.0136e-020.1827image
ENSG00000167088.9,SNRPD1PCPGEAGDendritic_cells_resting3.0136e-020.1827image
ENSG00000167088.9,SNRPD1READEAGEosinophils1.0277e-020.5597image
chr18:21630458-21633160:+SARCEERNeutrophils3.9631e-040.4064image
ENSG00000167088.9,SNRPD1SARCEAGNeutrophils3.9631e-040.4064image
chr18:21630458-21633160:+SKCMEERT_cells_regulatory_(Tregs)1.0076e-020.2023image
ENSG00000167088.9,SNRPD1SKCMEAGT_cells_regulatory_(Tregs)1.0076e-020.2023image
chr18:21630458-21633160:+STADEERT_cells_CD4_naive6.2825e-03-0.1951image
ENSG00000167088.9,SNRPD1STADEAGEosinophils5.0138e-03-0.1982image
chr18:21630458-21633160:+THCAEERMast_cells_resting1.6211e-02-0.1785image
ENSG00000167088.9,SNRPD1THCAEAGMast_cells_resting1.6211e-02-0.1785image
chr18:21630458-21633160:+UVMEERT_cells_CD83.6302e-020.4386image
ENSG00000167088.9,SNRPD1UVMEAGT_cells_CD83.6302e-020.4386image


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6. Enriched editing regions and immune gene sets for SNRPD1


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
chr18:21630458-21633160:+BLCAGSVA_HALLMARK_COAGULATIONEER5.1554e-030.3263image
ENSG00000167088.9,SNRPD1BLCAGSVA_HALLMARK_COAGULATIONEAG5.3524e-030.3250image
chr18:21630458-21633160:+BRCAGSVA_HALLMARK_PANCREAS_BETA_CELLSEER4.3585e-030.1394image
ENSG00000167088.9,SNRPD1BRCAGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG4.3103e-030.1395image
ENSG00000167088.9,SNRPD1CESCGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG7.2839e-040.3636image
ENSG00000167088.9,SNRPD1COADGSVA_HALLMARK_GLYCOLYSISEAG4.4079e-02-0.2487image
chr18:21630458-21633160:+COADGSVA_HALLMARK_GLYCOLYSISEER2.6404e-02-0.2754image
ENSG00000167088.9,SNRPD1GBMGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG2.3970e-030.2682image
chr18:21630458-21633160:+GBMGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER2.3970e-030.2682image
chr18:21630458-21633160:+HNSCGSVA_HALLMARK_E2F_TARGETSEER3.5530e-02-0.2416image
ENSG00000167088.9,SNRPD1HNSCGSVA_HALLMARK_E2F_TARGETSEAG3.5530e-02-0.2416image
ENSG00000167088.9,SNRPD1KICHGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG1.5404e-020.4886image
ENSG00000167088.9,SNRPD1KIRCGSVA_HALLMARK_UV_RESPONSE_DNEAG4.0882e-02-0.2049image
ENSG00000167088.9,SNRPD1KIRPGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEAG1.7669e-020.4703image
chr18:21630458-21633160:+KIRPGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEER1.7669e-020.4703image
ENSG00000167088.9,SNRPD1LGGGSVA_HALLMARK_MYOGENESISEAG1.8391e-050.1976image
chr18:21630458-21633160:+LGGGSVA_HALLMARK_MYOGENESISEER1.8391e-050.1976image
ENSG00000167088.9,SNRPD1LIHCGSVA_HALLMARK_PROTEIN_SECRETIONEAG1.5857e-02-0.5077image
ENSG00000167088.9,SNRPD1LUADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG3.3062e-020.2249image
chr18:21630458-21633160:+LUADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER3.3062e-020.2249image
ENSG00000167088.9,SNRPD1LUSCGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG2.7971e-03-0.2563image
chr18:21630458-21633160:+LUSCGSVA_HALLMARK_TGF_BETA_SIGNALINGEER2.2578e-03-0.2636image
chr18:21630458-21633160:+OVGSVA_HALLMARK_MYC_TARGETS_V1EER9.6457e-040.3300image
ENSG00000167088.9,SNRPD1OVGSVA_HALLMARK_MYC_TARGETS_V1EAG3.1457e-040.3531image
ENSG00000167088.9,SNRPD1PCPGGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG1.5895e-020.2028image
chr18:21630458-21633160:+PCPGGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER1.5895e-020.2028image
ENSG00000167088.9,SNRPD1READGSVA_HALLMARK_UV_RESPONSE_DNEAG6.6164e-040.6955image
ENSG00000167088.9,SNRPD1SARCGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG3.5323e-040.4096image
chr18:21630458-21633160:+SARCGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER3.5323e-040.4096image
ENSG00000167088.9,SNRPD1SKCMGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG3.3742e-030.2297image
chr18:21630458-21633160:+SKCMGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER3.3742e-030.2297image
chr18:21630458-21633160:+STADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER5.4013e-030.1985image
ENSG00000167088.9,SNRPD1STADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG5.3769e-030.1966image
chr18:21630458-21633160:+TGCTGSVA_HALLMARK_SPERMATOGENESISEER5.2978e-030.4003image
ENSG00000167088.9,SNRPD1TGCTGSVA_HALLMARK_SPERMATOGENESISEAG5.2978e-030.4003image
chr18:21630458-21633160:+THCAGSVA_HALLMARK_ANDROGEN_RESPONSEEER2.2751e-020.1692image
ENSG00000167088.9,SNRPD1THCAGSVA_HALLMARK_ANDROGEN_RESPONSEEAG2.2751e-020.1692image
ENSG00000167088.9,SNRPD1THYMGSVA_HALLMARK_ANDROGEN_RESPONSEEAG1.6497e-05-0.4966image
chr18:21630458-21633160:+THYMGSVA_HALLMARK_ANDROGEN_RESPONSEEER1.6497e-05-0.4966image
chr18:21630458-21633160:+UCECGSVA_HALLMARK_PROTEIN_SECRETIONEER3.9999e-02-0.3904image


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7. Enriched editing regions and drugs for SNRPD1


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
chr18:21630458-21633160:+BLCAGSK269962AEER5.1858e-03-0.3261image
ENSG00000167088.9,SNRPD1BLCAGSK269962AEAG5.3200e-03-0.3252image
ENSG00000167088.9,SNRPD1BRCAABT.263EAG1.0952e-030.1597image
chr18:21630458-21633160:+BRCAABT.263EER1.1308e-030.1593image
ENSG00000167088.9,SNRPD1CESCEHT.1864EAG3.9912e-02-0.2260image
ENSG00000167088.9,SNRPD1COADGefitinibEAG2.1373e-04-0.4406image
chr18:21630458-21633160:+COADGefitinibEER2.3042e-04-0.4417image
ENSG00000167088.9,SNRPD1GBMLapatinibEAG1.8687e-03-0.2745image
chr18:21630458-21633160:+GBMLapatinibEER1.8687e-03-0.2745image
chr18:21630458-21633160:+HNSCBortezomibEER2.9660e-020.2496image
ENSG00000167088.9,SNRPD1HNSCBortezomibEAG2.9660e-020.2496image
ENSG00000167088.9,SNRPD1KICHErlotinibEAG7.7130e-05-0.7183image
chr18:21630458-21633160:+KIRCGNF.2EER1.4389e-02-0.2466image
ENSG00000167088.9,SNRPD1KIRCCGP.082996EAG1.3350e-02-0.2467image
ENSG00000167088.9,SNRPD1KIRPEtoposideEAG1.6986e-020.4728image
chr18:21630458-21633160:+KIRPEtoposideEER1.6986e-020.4728image
ENSG00000167088.9,SNRPD1LGGKU.55933EAG1.2323e-08-0.2608image
chr18:21630458-21633160:+LGGKU.55933EER1.2323e-08-0.2608image
chr18:21630458-21633160:+LIHCElesclomolEER2.9209e-02-0.4759image
ENSG00000167088.9,SNRPD1LIHCBMS.708163EAG3.1760e-040.6964image
ENSG00000167088.9,SNRPD1LUADAZD8055EAG6.5863e-030.2844image
chr18:21630458-21633160:+LUADAZD8055EER6.5863e-030.2844image
chr18:21630458-21633160:+LUSCGW843682XEER1.3621e-02-0.2143image
ENSG00000167088.9,SNRPD1LUSCMidostaurinEAG1.3238e-020.2135image
chr18:21630458-21633160:+OVBexaroteneEER3.8745e-030.2907image
ENSG00000167088.9,SNRPD1OVBexaroteneEAG3.1313e-030.2926image
chr18:21630458-21633160:+PAADAZD7762EER2.1836e-030.5076image
ENSG00000167088.9,SNRPD1PAADAZD7762EAG2.1836e-030.5076image
chr18:21630458-21633160:+PCPGMethotrexateEER4.7424e-02-0.1673image
ENSG00000167088.9,SNRPD1PCPGMethotrexateEAG4.7424e-02-0.1673image
chr18:21630458-21633160:+PRADJNJ.26854165EER2.2654e-020.2647image
ENSG00000167088.9,SNRPD1PRADJNJ.26854165EAG2.3992e-020.2622image
ENSG00000167088.9,SNRPD1READGW.441756EAG1.4401e-020.5380image
chr18:21630458-21633160:+SARCDoxorubicinEER2.2694e-030.3542image
ENSG00000167088.9,SNRPD1SARCDoxorubicinEAG2.2694e-030.3542image
chr18:21630458-21633160:+SKCMGefitinibEER1.0412e-03-0.2561image
ENSG00000167088.9,SNRPD1SKCMGefitinibEAG1.0412e-03-0.2561image
chr18:21630458-21633160:+STADDocetaxelEER6.5337e-03-0.1942image
ENSG00000167088.9,SNRPD1STADDocetaxelEAG1.1996e-02-0.1778image
ENSG00000167088.9,SNRPD1TGCTAZD.0530EAG7.5430e-030.3850image
chr18:21630458-21633160:+TGCTAZD.0530EER7.5430e-030.3850image
chr18:21630458-21633160:+THCABMS.708163EER4.1178e-03-0.2123image
ENSG00000167088.9,SNRPD1THCABMS.708163EAG4.1178e-03-0.2123image
ENSG00000167088.9,SNRPD1THYMDMOGEAG1.5857e-040.4424image
chr18:21630458-21633160:+THYMDMOGEER1.5857e-040.4424image
ENSG00000167088.9,SNRPD1UCECBMS.754807EAG5.0745e-06-0.7372image
chr18:21630458-21633160:+UCECBMS.754807EER5.3571e-06-0.7453image
ENSG00000167088.9,SNRPD1UVMFTI.277EAG2.4879e-020.4664image
chr18:21630458-21633160:+UVMFTI.277EER2.4879e-020.4664image


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