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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: DEAF1 (ImmuneEditome ID:10522)

1. Gene summary of enriched editing regions for DEAF1

check button Gene summary
Gene informationGene symbol

DEAF1

Gene ID

10522

GeneSynonymsMRD24|NEDHELS|NUDR|SPN|VSVS|ZMYND5
GeneCytomap

11p15.5

GeneTypeprotein-coding
GeneDescriptiondeformed epidermal autoregulatory factor 1 homolog|nuclear DEAF-1-related transcriptional regulator|suppressin|zinc finger MYND domain-containing protein 5
GeneModificationdate20230517
UniprotIDO75398;A0A8I5KUA2;A0A8I5QL28;A0A804HIS1;A0A8I5KQJ8;A0A8I5QJC6;A0A8I5KQY1;H0YCY2;A0A8I5KZ80;A0A8I5KR93
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr11:645364-647096:-ENST00000527658.1ENSG00000177030.15DEAF1ncRNA_exonicAluSz6,AluJb,AluSpchr11:645364-647096:-.alignment
chr11:649286-652587:-ENST00000527170.4ENSG00000177030.15DEAF1exonic(TTTA)n,AluSx1,AluY,AluSz,L1M4,FLAM_C,AluJo,AluSx,AluSz6chr11:649286-652587:-.alignment
chr11:654258-654963:-ENST00000525904.4ENSG00000177030.15DEAF1ncRNA_intronicAluSx1,AluY,AluSg7chr11:654258-654963:-.alignment
chr11:654258-654963:-ENST00000530813.1ENSG00000177030.15DEAF1ncRNA_intronicAluSx1,AluY,AluSg7chr11:654258-654963:-.alignment
chr11:681258-681624:-ENST00000530813.1ENSG00000177030.15DEAF1ncRNA_intronicAluY,AluSqchr11:681258-681624:-.alignment


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2. Tumor-specific enriched editing regions for DEAF1


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
chr11:649286-652587:-THCAEER1.5112e-03image
ENSG00000177030.15,DEAF1THCAEAG1.7240e-03image


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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 DEAF1


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
chr11:649286-652587:-OVEERENSG00000242640,RP11-302F12.10.30186.0794e-049.5663e-110.4186imageNNNAMacrophages_M2GSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALING

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4. Enriched editing regions and immune related splicing for DEAF1


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
chr11:649286-652587:-
OVEERA3ENSG00000164877.14chr71450239:1450288:1448619:1448761:1448619:1449829-0.41562.4472e-071.6961e-10-0.4215imageNCELF2;DHX9;ELAVL1;ELAVL3;FBL;FUS;HNRNPA1;HNRNPC;IGF2BP2;ILF3;KHDRBS1;KHSRP;MOV10;NOP56;NOP58;PTBP1;RBFOX2;RBM27;TARDBP;U2AF1;U2AF2;UPF1;VIMMICALL2B_cells_memoryGSVA_HALLMARK_MITOTIC_SPINDLE
ENSG00000177030.15,DEAF1
OVEAGA3ENSG00000164877.14chr71450239:1450288:1448619:1448761:1448619:1449829-0.40325.2175e-072.0282e-10-0.4190imageNACIN1;ADAR;AIFM1;AUH;BCCIP;BUD13;CELF2;CPSF6;CSTF2T;DDX3X;DDX54;DGCR8;DHX9;DKC1;EIF4A3;EIF4G2;ELAVL1;ELAVL3;EWSR1;FAM120A;FBL;FMR1;FUS;FXR1;FXR2;GNL3;GTF2F1;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPK;HNRNPM;HNRNPU;HNRNPUL1;IGF2BP1;IGF2BP2;IGF2BP3;ILF3;KHDRBS1;KHSRP;LARP7;LIN28;LIN28B;METTL3;MOV10;MSI1;MSI2;NONO;NOP56;NOP58;NPM1;NUMA1;PCBP2;PRPF8;PTBP1;RANGAP1;RBFOX2;RBM10;RBM22;RBM27;SAFB2;SBDS;SF3A3;SF3B4;SLBP;SLTM;SMNDC1;SND1;SRSF1;SRSF7;SRSF9;TAF15;TARDBP;TIA1;TNRC6A;TROVE2;U2AF1;U2AF2;UPF1;VIM;XRN2;YTHDC1;YTHDF1;ZNF184MICALL2B_cells_memoryGSVA_HALLMARK_MITOTIC_SPINDLE

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5. Enriched editing regions and immune infiltration for DEAF1


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
chr11:649286-652587:-BLCAEERNK_cells_activated4.8835e-030.3503image
ENSG00000177030.15,DEAF1BLCAEAGNK_cells_activated1.7584e-020.2937image
chr11:649286-652587:-BRCAEERMast_cells_resting3.7563e-02-0.1506image
chr11:649286-652587:-CESCEERPlasma_cells1.8099e-030.4572image
ENSG00000177030.15,DEAF1CESCEAGPlasma_cells1.0411e-020.3628image
chr11:649286-652587:-ESCAEERB_cells_naive2.5379e-02-0.2343image
chr11:649286-652587:-GBMEERDendritic_cells_activated3.0961e-020.2861image
ENSG00000177030.15,DEAF1GBMEAGEosinophils1.7139e-020.3146image
chr11:649286-652587:-HNSCEERMonocytes8.4694e-030.4575image
ENSG00000177030.15,DEAF1HNSCEAGMonocytes7.8637e-030.4546image
chr11:649286-652587:-KIRCEERT_cells_gamma_delta4.4252e-020.1996image
ENSG00000177030.15,DEAF1KIRCEAGT_cells_gamma_delta1.8707e-020.2249image
ENSG00000177030.15,DEAF1LAMLEAGNK_cells_activated4.6315e-030.3301image
chr11:649286-652587:-LGGEERB_cells_memory1.1965e-020.1587image
ENSG00000177030.15,DEAF1LGGEAGB_cells_memory3.5723e-020.1324image
chr11:649286-652587:-LIHCEERT_cells_regulatory_(Tregs)1.1401e-020.5406image
ENSG00000177030.15,DEAF1LIHCEAGT_cells_regulatory_(Tregs)2.8871e-030.5926image
chr11:649286-652587:-LUADEERMast_cells_activated3.9259e-02-0.1969image
ENSG00000177030.15,DEAF1LUADEAGMast_cells_activated3.9895e-02-0.1945image
chr11:649286-652587:-LUSCEERB_cells_memory4.9492e-030.2519image
ENSG00000177030.15,DEAF1LUSCEAGMacrophages_M03.7951e-03-0.2571image
chr11:645364-647096:-OVEERT_cells_CD4_naive2.2225e-020.3136image
chr11:649286-652587:-OVEERT_cells_CD4_memory_activated8.4670e-040.2234image
ENSG00000177030.15,DEAF1OVEAGT_cells_CD4_memory_activated6.9579e-040.2264image
chr11:649286-652587:-PRADEERDendritic_cells_activated6.6645e-040.3466image
ENSG00000177030.15,DEAF1PRADEAGDendritic_cells_activated5.7500e-040.3486image
chr11:649286-652587:-SARCEERNK_cells_activated2.3968e-020.3479image
ENSG00000177030.15,DEAF1SARCEAGNK_cells_activated1.3328e-020.3790image
chr11:649286-652587:-SKCMEERDendritic_cells_resting9.7563e-030.2234image
ENSG00000177030.15,DEAF1SKCMEAGDendritic_cells_resting1.1398e-020.2188image
chr11:649286-652587:-STADEERT_cells_CD4_memory_activated2.4047e-020.1772image
ENSG00000177030.15,DEAF1STADEAGNK_cells_resting4.9733e-020.1457image
chr11:649286-652587:-THYMEERT_cells_regulatory_(Tregs)7.3612e-030.5130image
ENSG00000177030.15,DEAF1THYMEAGT_cells_regulatory_(Tregs)6.8208e-030.5172image
chr11:649286-652587:-UCECEERNeutrophils3.9081e-02-0.3053image
ENSG00000177030.15,DEAF1UCECEAGNeutrophils4.4405e-02-0.2856image
chr11:649286-652587:-UCSEERDendritic_cells_resting7.1529e-040.6208image
ENSG00000177030.15,DEAF1UCSEAGDendritic_cells_resting7.4046e-040.6194image
chr11:649286-652587:-UVMEEREosinophils4.2591e-020.3665image
ENSG00000177030.15,DEAF1UVMEAGEosinophils4.2591e-020.3665image


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6. Enriched editing regions and immune gene sets for DEAF1


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
chr11:649286-652587:-BLCAGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER2.3891e-02-0.2844image
chr11:649286-652587:-BRCAGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEER1.5457e-030.2276image
ENSG00000177030.15,DEAF1BRCAGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG2.0573e-040.2615image
ENSG00000177030.15,DEAF1CESCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG4.2833e-02-0.2906image
chr11:649286-652587:-CESCGSVA_HALLMARK_NOTCH_SIGNALINGEER2.6964e-02-0.3335image
chr11:649286-652587:-ESCAGSVA_HALLMARK_MITOTIC_SPINDLEEER9.1830e-03-0.2717image
ENSG00000177030.15,DEAF1ESCAGSVA_HALLMARK_G2M_CHECKPOINTEAG8.1102e-03-0.2660image
ENSG00000177030.15,DEAF1KIRCGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEAG1.1108e-020.2424image
chr11:649286-652587:-KIRCGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEER3.9170e-020.2046image
chr11:649286-652587:-LAMLGSVA_HALLMARK_SPERMATOGENESISEER2.6888e-02-0.2932image
chr11:649286-652587:-LGGGSVA_HALLMARK_KRAS_SIGNALING_DNEER1.3417e-030.2017image
ENSG00000177030.15,DEAF1LGGGSVA_HALLMARK_KRAS_SIGNALING_UPEAG1.6199e-030.1976image
ENSG00000177030.15,DEAF1LIHCGSVA_HALLMARK_E2F_TARGETSEAG2.3134e-04-0.6952image
chr11:649286-652587:-LIHCGSVA_HALLMARK_E2F_TARGETSEER6.2873e-04-0.6840image
chr11:649286-652587:-LUADGSVA_HALLMARK_P53_PATHWAYEER1.1261e-020.2408image
ENSG00000177030.15,DEAF1LUADGSVA_HALLMARK_P53_PATHWAYEAG1.4848e-020.2297image
chr11:649286-652587:-LUSCGSVA_HALLMARK_ADIPOGENESISEER8.2804e-040.2976image
ENSG00000177030.15,DEAF1LUSCGSVA_HALLMARK_ADIPOGENESISEAG6.5726e-040.3006image
chr11:649286-652587:-OVGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER1.4318e-040.2536image
chr11:645364-647096:-OVGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEER2.4996e-020.3077image
ENSG00000177030.15,DEAF1OVGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG6.1855e-050.2661image
ENSG00000177030.15,DEAF1SARCGSVA_HALLMARK_BILE_ACID_METABOLISMEAG4.9923e-020.3045image
ENSG00000177030.15,DEAF1SKCMGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG3.6340e-02-0.1817image
chr11:649286-652587:-SKCMGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER3.9236e-02-0.1790image
chr11:649286-652587:-STADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER1.3038e-020.1947image
ENSG00000177030.15,DEAF1STADGSVA_HALLMARK_P53_PATHWAYEAG5.0707e-040.2552image
ENSG00000177030.15,DEAF1THCAGSVA_HALLMARK_KRAS_SIGNALING_UPEAG6.4328e-03-0.2126image
chr11:649286-652587:-THCAGSVA_HALLMARK_KRAS_SIGNALING_UPEER6.2650e-03-0.2139image
ENSG00000177030.15,DEAF1THYMGSVA_HALLMARK_XENOBIOTIC_METABOLISMEAG1.6547e-03-0.5861image
chr11:649286-652587:-THYMGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER1.6944e-03-0.5850image
chr11:649286-652587:-UCECGSVA_HALLMARK_MITOTIC_SPINDLEEER4.9396e-02-0.2914image
ENSG00000177030.15,DEAF1UCSGSVA_HALLMARK_BILE_ACID_METABOLISMEAG2.9952e-020.4261image
chr11:649286-652587:-UCSGSVA_HALLMARK_BILE_ACID_METABOLISMEER2.9449e-020.4273image
ENSG00000177030.15,DEAF1UVMGSVA_HALLMARK_IL6_JAK_STAT3_SIGNALINGEAG3.0264e-02-0.3896image
chr11:649286-652587:-UVMGSVA_HALLMARK_IL6_JAK_STAT3_SIGNALINGEER3.0264e-02-0.3896image


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7. Enriched editing regions and drugs for DEAF1


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
chr11:649286-652587:-BLCAEmbelinEER1.2996e-020.3114image
ENSG00000177030.15,DEAF1BLCAEmbelinEAG2.0749e-020.2864image
ENSG00000177030.15,DEAF1BRCAGNF.2EAG4.9863e-03-0.1993image
chr11:649286-652587:-BRCACCT007093EER8.7804e-030.1891image
ENSG00000177030.15,DEAF1CESCCMKEAG1.6941e-020.3397image
chr11:649286-652587:-CESCCMKEER3.6761e-020.3158image
ENSG00000177030.15,DEAF1ESCAKU.55933EAG9.4454e-04-0.3289image
chr11:649286-652587:-ESCAKU.55933EER3.7096e-05-0.4182image
chr11:649286-652587:-HNSCABT.888EER3.0933e-02-0.3821image
ENSG00000177030.15,DEAF1HNSCABT.888EAG2.7239e-02-0.3843image
ENSG00000177030.15,DEAF1KIRCGefitinibEAG2.8205e-030.2834image
chr11:649286-652587:-KIRCGefitinibEER1.2412e-020.2468image
ENSG00000177030.15,DEAF1KIRPEHT.1864EAG1.5015e-020.2234image
chr11:649286-652587:-KIRPEHT.1864EER1.5736e-020.2228image
chr11:649286-652587:-LAMLABT.888EER2.7734e-030.3892image
ENSG00000177030.15,DEAF1LAMLGDC0941EAG3.0422e-020.2553image
ENSG00000177030.15,DEAF1LGGBAY.61.3606EAG5.6791e-040.2156image
chr11:649286-652587:-LGGGSK.650394EER5.1908e-040.2180image
ENSG00000177030.15,DEAF1LIHCAZ628EAG4.7774e-02-0.4265image
ENSG00000177030.15,DEAF1LUADAZD7762EAG4.7014e-02-0.1881image
chr11:649286-652587:-LUSCCHIR.99021EER5.5493e-040.3069image
ENSG00000177030.15,DEAF1LUSCCHIR.99021EAG4.5851e-040.3088image
ENSG00000177030.15,DEAF1OVEmbelinEAG1.2178e-050.2896image
chr11:649286-652587:-OVEmbelinEER1.3506e-050.2888image
chr11:645364-647096:-OVAMG.706EER1.0584e-020.3484image
ENSG00000177030.15,DEAF1PRADBAY.61.3606EAG1.4311e-050.4312image
chr11:649286-652587:-PRADBAY.61.3606EER8.8790e-060.4426image
ENSG00000177030.15,DEAF1SARCBIBW2992EAG9.1157e-03-0.3976image
chr11:649286-652587:-SARCBIBW2992EER1.1800e-02-0.3850image
ENSG00000177030.15,DEAF1SKCMEHT.1864EAG1.6033e-020.2085image
chr11:649286-652587:-SKCMEHT.1864EER1.7057e-020.2066image
chr11:649286-652587:-STADBortezomibEER8.3035e-03-0.2067image
ENSG00000177030.15,DEAF1STADAZD6244EAG2.7919e-02-0.1630image
chr11:649286-652587:-THCAGW.441756EER2.4131e-03-0.2368image
ENSG00000177030.15,DEAF1THCAGW.441756EAG2.1841e-03-0.2384image
chr11:649286-652587:-THYMAS601245EER5.9540e-030.5244image
ENSG00000177030.15,DEAF1THYMAS601245EAG3.5306e-030.5510image
chr11:649286-652587:-UCSMetforminEER2.5017e-02-0.4386image
ENSG00000177030.15,DEAF1UCSBIBW2992EAG2.3838e-02-0.4418image


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