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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: LSM14A (ImmuneEditome ID:26065)

1. Gene summary of enriched editing regions for LSM14A

check button Gene summary
Gene informationGene symbol

LSM14A

Gene ID

26065

GeneSynonymsC19orf13|FAM61A|RAP55|RAP55A
GeneCytomap

19q13.11

GeneTypeprotein-coding
GeneDescriptionprotein LSM14 homolog A|LSM14 homolog A|LSM14A, SCD6 homolog A|RNA-associated protein 55|RNA-associated protein 55A|alphaSNBP|family with sequence similarity 61, member A|hRAP55|hRAP55A|protein SCD6 homolog|putative alpha-synuclein-binding protein
GeneModificationdate20230329
UniprotIDQ8ND56;I3L4Q1;K7EMZ9;A0A140TA66;A0A140TA76;A0A0G2JQ95
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr19:34192376-34194131:+ENST00000433627.8ENSG00000257103.7LSM14AintronicAluSz,Charlie18a,AluJb,(A)nchr19:34192376-34194131:+.alignment
chr19:34192376-34194131:+ENST00000540746.5ENSG00000257103.7LSM14AintronicAluSz,Charlie18a,AluJb,(A)nchr19:34192376-34194131:+.alignment
chr19:34192376-34194131:+ENST00000544216.6ENSG00000257103.7LSM14AintronicAluSz,Charlie18a,AluJb,(A)nchr19:34192376-34194131:+.alignment
chr19:34192376-34194131:+ENST00000586157.2ENSG00000257103.7LSM14AintronicAluSz,Charlie18a,AluJb,(A)nchr19:34192376-34194131:+.alignment
chr19:34192376-34194131:+ENST00000589878.4ENSG00000257103.7LSM14AintronicAluSz,Charlie18a,AluJb,(A)nchr19:34192376-34194131:+.alignment
chr19:34198385-34199401:+ENST00000433627.8ENSG00000257103.7LSM14AintronicAluSp,AluY,(TTAT)n,L1MC5,AluSzchr19:34198385-34199401:+.alignment
chr19:34198385-34199401:+ENST00000540746.5ENSG00000257103.7LSM14AintronicAluSp,AluY,(TTAT)n,L1MC5,AluSzchr19:34198385-34199401:+.alignment
chr19:34198385-34199401:+ENST00000544216.6ENSG00000257103.7LSM14AintronicAluSp,AluY,(TTAT)n,L1MC5,AluSzchr19:34198385-34199401:+.alignment
chr19:34198385-34199401:+ENST00000586157.2ENSG00000257103.7LSM14AintronicAluSp,AluY,(TTAT)n,L1MC5,AluSzchr19:34198385-34199401:+.alignment
chr19:34201363-34207802:+ENST00000433627.8ENSG00000257103.7LSM14AintronicL1MC,AluSx3,AluJo,AluJb,AluJr,(T)n,L1M5,AluSx4,AluSg,L3,AluSz,AluSx1,(TTTTG)n,AluYchr19:34201363-34207802:+.alignment
chr19:34201363-34207802:+ENST00000540746.5ENSG00000257103.7LSM14AintronicL1MC,AluSx3,AluJo,AluJb,AluJr,(T)n,L1M5,AluSx4,AluSg,L3,AluSz,AluSx1,(TTTTG)n,AluYchr19:34201363-34207802:+.alignment
chr19:34201363-34207802:+ENST00000544216.6ENSG00000257103.7LSM14AintronicL1MC,AluSx3,AluJo,AluJb,AluJr,(T)n,L1M5,AluSx4,AluSg,L3,AluSz,AluSx1,(TTTTG)n,AluYchr19:34201363-34207802:+.alignment
chr19:34201363-34207802:+ENST00000586157.2ENSG00000257103.7LSM14AintronicL1MC,AluSx3,AluJo,AluJb,AluJr,(T)n,L1M5,AluSx4,AluSg,L3,AluSz,AluSx1,(TTTTG)n,AluYchr19:34201363-34207802:+.alignment
chr19:34210387-34211763:+ENST00000588582.3ENSG00000257103.7LSM14AncRNA_intronicAluSz,AluSx,AluJbchr19:34210387-34211763:+.alignment
chr19:34212955-34214499:+ENST00000588582.3ENSG00000257103.7LSM14AncRNA_intronic(T)n,AluJb,AluJr4,AluSzchr19:34212955-34214499:+.alignment
chr19:34216550-34218198:+ENST00000588582.3ENSG00000257103.7LSM14AncRNA_intronicAluSx4,(AT)n,AluSx3,AluSq,AluYcchr19:34216550-34218198:+.alignment
chr19:34223101-34224260:+ENST00000588582.3ENSG00000257103.7LSM14AncRNA_intronicX6A_LINE,AluJr,AluSx,L3chr19:34223101-34224260:+.alignment
chr19:34223101-34224260:+ENST00000590416.1ENSG00000257103.7LSM14AncRNA_intronicX6A_LINE,AluJr,AluSx,L3chr19:34223101-34224260:+.alignment
chr19:34225798-34226012:+ENST00000588582.3ENSG00000257103.7LSM14AncRNA_intronicAluJochr19:34225798-34226012:+.alignment
chr19:34225798-34226012:+ENST00000590416.1ENSG00000257103.7LSM14AncRNA_intronicAluJochr19:34225798-34226012:+.alignment


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2. Tumor-specific enriched editing regions for LSM14A


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 LSM14A


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

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4. Enriched editing regions and immune related splicing for LSM14A


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
chr19:34201363-34207802:+
ESCAEERIRENSG00000002016.12chr12929763:929886:930050:930144-0.34082.8788e-021.3089e-05-0.4131imageNCNBP;DHX9;DKC1;ELAVL1;FBL;FUS;HNRNPC;HNRNPK;HNRNPL;IGF2BP2;NOP56;NOP58;PTBP1;RBFOX2;TAF15;TARDBPNAMacrophages_M2GSVA_HALLMARK_GLYCOLYSIS
ENSG00000257103.7,LSM14A
ESCAEAGIRENSG00000047346.8chr1552584742:52584944:52587055:52587219-0.30413.3308e-029.6593e-06-0.4285imageNACIN1;ADAR;AIFM1;ALYREF;AUH;BCCIP;BUD13;CELF2;CNBP;CPSF6;CSTF2T;DDX3X;DDX42;DDX54;DGCR8;DHX9;DKC1;EIF4A3;EIF4G2;ELAVL1;ELAVL3;EWSR1;FAM120A;FBL;FMR1;FTO;FUS;FXR1;FXR2;GTF2F1;HNRNPA1;HNRNPA2B1;HNRNPC;HNRNPD;HNRNPK;HNRNPL;HNRNPM;IGF2BP1;IGF2BP2;IGF2BP3;KHDRBS1;KHDRBS2;KHDRBS3;KHSRP;LARP7;LIN28;LIN28A;LIN28B;LSM11;MBNL2;METTL3;MOV10;MSI1;MSI2;NONO;NOP56;NOP58;NUMA1;PCBP2;PRPF8;PTBP1;PUM2;QKI;RANGAP1;RBFOX2;RBM10;RBM22;RBM47;RBM5;SAFB2;SF3A3;SF3B4;SLTM;SMNDC1;SND1;SRSF1;SRSF10;SRSF3;SRSF7;SRSF9;TAF15;TARBP2;TARDBP;TIA1;TIAL1;TNRC6A;TRA2A;TROVE2;U2AF1;U2AF2;UPF1;XRN2;YTHDC1;YTHDF1;ZNF184NANK_cells_activatedGSVA_HALLMARK_GLYCOLYSIS
chr19:34201363-34207802:+
ESCAEERIRENSG00000128833.8chr1552246916:52247014:52247457:52247522-0.31623.1733e-023.8697e-05-0.4031imageNCNBP;DHX9;DKC1;ELAVL1;FBL;FUS;HNRNPC;HNRNPK;HNRNPL;IGF2BP2;NOP56;NOP58;PTBP1;RBFOX2;TAF15;TARDBPNAT_cells_CD4_naiveGSVA_HALLMARK_ADIPOGENESIS

More results



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5. Enriched editing regions and immune infiltration for LSM14A


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
ENSG00000257103.7,LSM14ABLCAEAGMonocytes2.5466e-020.4292image
ENSG00000257103.7,LSM14ABRCAEAGT_cells_CD4_memory_resting3.2933e-02-0.2289image
chr19:34198385-34199401:+ESCAEERNeutrophils1.1526e-030.4740image
chr19:34216550-34218198:+ESCAEERT_cells_regulatory_(Tregs)1.7546e-03-0.4198image
chr19:34223101-34224260:+ESCAEERMacrophages_M24.6519e-020.2478image
ENSG00000257103.7,LSM14AKIRCEAGNeutrophils2.8318e-020.2622image
ENSG00000257103.7,LSM14AKIRPEAGT_cells_regulatory_(Tregs)7.5038e-030.4709image
ENSG00000257103.7,LSM14ALAMLEAGMast_cells_resting4.8077e-020.1832image
ENSG00000257103.7,LSM14ALUADEAGT_cells_gamma_delta4.5589e-02-0.3263image
ENSG00000257103.7,LSM14ALUSCEAGB_cells_naive7.9265e-040.5092image
chr19:34192376-34194131:+OVEERB_cells_memory2.1588e-02-0.3669image
chr19:34201363-34207802:+OVEERMonocytes2.5722e-020.1691image
ENSG00000257103.7,LSM14AOVEAGMast_cells_activated2.7566e-020.1547image
ENSG00000257103.7,LSM14APRADEAGT_cells_CD4_memory_activated1.4234e-020.4359image
chr19:34192376-34194131:+STADEERT_cells_CD4_memory_activated4.3944e-020.2166image
chr19:34198385-34199401:+STADEERMast_cells_activated3.3900e-030.3505image
chr19:34201363-34207802:+STADEERT_cells_CD4_memory_activated1.2621e-040.2665image
chr19:34216550-34218198:+STADEERNeutrophils1.0868e-020.2347image
chr19:34223101-34224260:+STADEERMacrophages_M12.8629e-020.2433image
ENSG00000257103.7,LSM14ASTADEAGT_cells_CD4_memory_activated2.7699e-020.1412image
ENSG00000257103.7,LSM14ATHCAEAGMast_cells_resting4.4683e-020.3756image


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6. Enriched editing regions and immune gene sets for LSM14A


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
chr19:34198385-34199401:+STADEER1.2899e-030.38241.1624e-020.30445.1237e-030.33581.6258e-020.2905image


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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
ENSG00000257103.7,LSM14ABLCAGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG2.4462e-020.4319image
ENSG00000257103.7,LSM14ABRCAGSVA_HALLMARK_GLYCOLYSISEAG3.0770e-050.4310image
chr19:34192376-34194131:+ESCAGSVA_HALLMARK_APOPTOSISEER1.6478e-020.3312image
ENSG00000257103.7,LSM14AESCAGSVA_HALLMARK_APOPTOSISEAG7.2130e-050.3336image
chr19:34223101-34224260:+ESCAGSVA_HALLMARK_KRAS_SIGNALING_UPEER2.1016e-030.3747image
chr19:34201363-34207802:+ESCAGSVA_HALLMARK_GLYCOLYSISEER3.7946e-030.2561image
chr19:34216550-34218198:+ESCAGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEER5.5001e-030.3762image
ENSG00000257103.7,LSM14AKIRCGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG6.6000e-030.3218image
ENSG00000257103.7,LSM14AKIRPGSVA_HALLMARK_KRAS_SIGNALING_DNEAG6.5216e-030.4781image
chr19:34201363-34207802:+LAMLGSVA_HALLMARK_PANCREAS_BETA_CELLSEER3.0134e-020.2576image
chr19:34192376-34194131:+OVGSVA_HALLMARK_ESTROGEN_RESPONSE_LATEEER4.7808e-020.3190image
ENSG00000257103.7,LSM14AOVGSVA_HALLMARK_DNA_REPAIREAG2.9012e-070.3507image
chr19:34201363-34207802:+OVGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEER9.8659e-050.2909image
chr19:34216550-34218198:+OVGSVA_HALLMARK_NOTCH_SIGNALINGEER2.7149e-020.2784image
chr19:34201363-34207802:+STADGSVA_HALLMARK_P53_PATHWAYEER8.0082e-080.3667image
chr19:34210387-34211763:+STADGSVA_HALLMARK_APOPTOSISEER8.3447e-030.4727image
chr19:34216550-34218198:+STADGSVA_HALLMARK_PROTEIN_SECRETIONEER8.0099e-030.2440image
chr19:34192376-34194131:+STADGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEER3.9622e-020.2211image
chr19:34198385-34199401:+STADGSVA_HALLMARK_APOPTOSISEER6.0576e-040.4053image
ENSG00000257103.7,LSM14ASTADGSVA_HALLMARK_P53_PATHWAYEAG1.2027e-050.2767image
chr19:34223101-34224260:+STADGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEER5.3193e-030.3069image


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7. Enriched editing regions and drugs for LSM14A


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
ENSG00000257103.7,LSM14ABRCAJNK.9LEAG7.0839e-040.3562image
chr19:34192376-34194131:+ESCACMKEER2.9257e-020.3025image
ENSG00000257103.7,LSM14AESCABIRB.0796EAG2.8001e-030.2544image
chr19:34223101-34224260:+ESCAGDC.0449EER1.7632e-02-0.2936image
chr19:34216550-34218198:+ESCABexaroteneEER6.2550e-03-0.3709image
ENSG00000257103.7,LSM14AKIRCCytarabineEAG1.5660e-020.2879image
chr19:34223101-34224260:+KIRCABT.263EER1.5358e-02-0.4124image
ENSG00000257103.7,LSM14AKIRPBAY.61.3606EAG1.3441e-030.5502image
ENSG00000257103.7,LSM14ALAMLJNK.9LEAG4.4204e-02-0.1864image
ENSG00000257103.7,LSM14ALUSCGNF.2EAG2.4251e-020.3558image
chr19:34192376-34194131:+OVCMKEER1.5390e-02-0.3854image
ENSG00000257103.7,LSM14AOVMG.132EAG3.0820e-05-0.2887image
chr19:34223101-34224260:+OVMG.132EER2.6348e-02-0.3752image
chr19:34201363-34207802:+OVLenalidomideEER2.6613e-040.2731image
ENSG00000257103.7,LSM14APRADFH535EAG3.7827e-030.5047image
chr19:34201363-34207802:+STADBMS.509744EER3.2535e-04-0.2504image
chr19:34210387-34211763:+STADMG.132EER3.5343e-02-0.3856image
chr19:34216550-34218198:+STADLenalidomideEER1.1116e-020.2340image
chr19:34192376-34194131:+STADAxitinibEER2.9810e-030.3148image
chr19:34198385-34199401:+STADDocetaxelEER1.4269e-02-0.2960image
ENSG00000257103.7,LSM14ASTADA.443654EAG3.6151e-03-0.1860image
chr19:34223101-34224260:+STADBMS.536924EER1.0325e-02-0.2835image
ENSG00000257103.7,LSM14ATHCAAG.014699EAG1.3021e-02-0.4555image


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