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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: STAG3L1 (ImmuneEditome ID:54441)

1. Gene summary of enriched editing regions for STAG3L1

check button Gene summary
Gene informationGene symbol

STAG3L1

Gene ID

54441

GeneSynonymsSTAG3L1P|STAG3L2|STAG3L3
GeneCytomap

7q11.23

GeneTypepseudo
GeneDescriptionSTAG3-like protein 1|stromal antigen 3-like 1 (pseudogene)
GeneModificationdate20230422
UniprotID.
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr7:75367194-75370008:+ENST00000404291.3ENSG00000205583.12STAG3L1ncRNA_intronicAluY,AluSx1,AluSp,ORSL,MIR,(CTCA)n,(CACACA)n,AluSz,AluSq2,L1MEd,AluSz6,FRAM,AluJrchr7:75367194-75370008:+.alignment
chr7:75367194-75370008:+ENST00000619870.3ENSG00000205583.12STAG3L1ncRNA_intronicAluY,AluSx1,AluSp,ORSL,MIR,(CTCA)n,(CACACA)n,AluSz,AluSq2,L1MEd,AluSz6,FRAM,AluJrchr7:75367194-75370008:+.alignment
chr7:75370646-75371780:+ENST00000404291.3ENSG00000205583.12STAG3L1ncRNA_intronicAluJb,AluJo,L1ME4a,AluSp,L1ME3Bchr7:75370646-75371780:+.alignment
chr7:75370646-75371780:+ENST00000619870.3ENSG00000205583.12STAG3L1ncRNA_intronicAluJb,AluJo,L1ME4a,AluSp,L1ME3Bchr7:75370646-75371780:+.alignment
chr7:75383043-75384146:+ENST00000404291.3ENSG00000205583.12STAG3L1ncRNA_intronicAluSz,AluSq2,MLT1I,AluSx1chr7:75383043-75384146:+.alignment
chr7:75383043-75384146:+ENST00000619870.3ENSG00000205583.12STAG3L1ncRNA_intronicAluSz,AluSq2,MLT1I,AluSx1chr7:75383043-75384146:+.alignment
chr7:75386125-75388125:+ENST00000404291.3ENSG00000205583.12STAG3L1ncRNA_intronicFLAM_A,MIRc,AluJr,MER50,(AT)n,AluSx,AluJo,(TAAA)n,AluSx1chr7:75386125-75388125:+.alignment
chr7:75386125-75388125:+ENST00000487154.1ENSG00000205583.12STAG3L1ncRNA_intronicFLAM_A,MIRc,AluJr,MER50,(AT)n,AluSx,AluJo,(TAAA)n,AluSx1chr7:75386125-75388125:+.alignment
chr7:75386125-75388125:+ENST00000619870.3ENSG00000205583.12STAG3L1ncRNA_intronicFLAM_A,MIRc,AluJr,MER50,(AT)n,AluSx,AluJo,(TAAA)n,AluSx1chr7:75386125-75388125:+.alignment


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2. Tumor-specific enriched editing regions for STAG3L1


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
chr7:75367194-75370008:+STADEER1.9320e-03image
ENSG00000205583.12,STAG3L1STADEAG2.6254e-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 STAG3L1


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 STAG3L1


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
ENSG00000205583.12,STAG3L1
GBMEAGIRENSG00000174953.9chr3154272545:154273905:154274046:154274140-0.23651.9692e-025.4106e-06-0.4238imageNNDHX36T_cells_CD4_naiveGSVA_HALLMARK_KRAS_SIGNALING_UP
chr7:75367194-75370008:+
GBMEERESENSG00000160256.8chr2144967033:44967181:44973199:44973265:44976679:44976973-0.34041.5863e-025.5439e-07-0.4417imageNCELF2;CSTF2T;DDX3X;DGCR8;EIF4A3;ELAVL1;FMR1;FUS;HNRNPC;LARP7;NOP56;PRPF8;RBFOX2;SF3B4;SRSF1;SRSF7;SRSF9;TAF15NAMonocytesGSVA_HALLMARK_BILE_ACID_METABOLISM
chr7:75367194-75370008:+
GBMEERIRENSG00000174953.9chr3154272545:154273905:154274046:154274140-0.23651.6955e-024.8235e-06-0.4258imageNAUH;BUD13;CELF2;CSTF2T;DDX3X;DGCR8;EIF4A3;ELAVL1;FAM120A;FMR1;FUS;FXR2;GTF2F1;HNRNPC;HNRNPU;NONO;NOP56;PRPF8;RBFOX2;SF3B4;SRSF1;SRSF7;SRSF9;TAF15;TIA1;U2AF1DHX36T_cells_CD4_naiveGSVA_HALLMARK_KRAS_SIGNALING_UP
ENSG00000205583.12,STAG3L1
GBMEAGESENSG00000160256.8chr2144967033:44967181:44973199:44973265:44976679:44976973-0.34431.6181e-023.4688e-07-0.4487imageNNNAMonocytesGSVA_HALLMARK_BILE_ACID_METABOLISM

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5. Enriched editing regions and immune infiltration for STAG3L1


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
chr7:75367194-75370008:+BLCAEERPlasma_cells4.1879e-020.2572image
ENSG00000205583.12,STAG3L1BRCAEAGMacrophages_M23.8057e-02-0.0954image
chr7:75367194-75370008:+COADEERPlasma_cells2.9085e-020.2918image
ENSG00000205583.12,STAG3L1COADEAGPlasma_cells1.7502e-020.3033image
chr7:75367194-75370008:+ESCAEERT_cells_CD4_memory_activated3.5350e-040.2807image
ENSG00000205583.12,STAG3L1ESCAEAGT_cells_CD4_memory_activated7.2902e-030.2127image
chr7:75367194-75370008:+GBMEERMonocytes4.0773e-03-0.2522image
ENSG00000205583.12,STAG3L1GBMEAGMonocytes3.7111e-03-0.2547image
chr7:75367194-75370008:+KICHEEREosinophils1.4955e-020.3530image
ENSG00000205583.12,STAG3L1KICHEAGEosinophils2.7375e-020.3219image
ENSG00000205583.12,STAG3L1KIRPEAGB_cells_naive3.6413e-020.1810image
chr7:75367194-75370008:+LAMLEERT_cells_gamma_delta1.3175e-030.3109image
ENSG00000205583.12,STAG3L1LAMLEAGT_cells_gamma_delta1.0745e-030.3119image
chr7:75367194-75370008:+LGGEERT_cells_CD4_memory_activated2.4732e-020.2033image
chr7:75370646-75371780:+LUADEERMacrophages_M17.2323e-030.5680image
ENSG00000205583.12,STAG3L1LUADEAGMonocytes2.4290e-030.2628image
chr7:75367194-75370008:+LUSCEERT_cells_gamma_delta4.2731e-020.1703image
chr7:75367194-75370008:+PCPGEERMast_cells_resting5.0033e-040.4464image
ENSG00000205583.12,STAG3L1PCPGEAGMast_cells_resting6.0894e-030.3560image
chr7:75367194-75370008:+PRADEERNK_cells_activated2.1016e-02-0.2169image
ENSG00000205583.12,STAG3L1PRADEAGDendritic_cells_activated4.2541e-02-0.1810image
ENSG00000205583.12,STAG3L1SARCEAGT_cells_CD84.9150e-030.4922image
chr7:75367194-75370008:+SKCMEERB_cells_memory2.5906e-020.1724image
ENSG00000205583.12,STAG3L1SKCMEAGB_cells_memory4.5236e-020.1478image
chr7:75367194-75370008:+THCAEEREosinophils6.5723e-030.2083image
ENSG00000205583.12,STAG3L1THCAEAGDendritic_cells_resting3.0245e-02-0.1602image
chr7:75367194-75370008:+UCECEERPlasma_cells2.0792e-020.4509image
ENSG00000205583.12,STAG3L1UCECEAGMacrophages_M18.7831e-03-0.4489image


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6. Enriched editing regions and immune gene sets for STAG3L1


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
ENSG00000205583.12,STAG3L1BRCAGSVA_HALLMARK_PROTEIN_SECRETIONEAG1.1368e-03-0.1492image
chr7:75367194-75370008:+BRCAGSVA_HALLMARK_P53_PATHWAYEER1.1312e-020.1196image
chr7:75367194-75370008:+CESCGSVA_HALLMARK_GLYCOLYSISEER1.7988e-02-0.4156image
ENSG00000205583.12,STAG3L1COADGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG1.7302e-030.3930image
chr7:75367194-75370008:+COADGSVA_HALLMARK_PANCREAS_BETA_CELLSEER2.5305e-030.3958image
chr7:75367194-75370008:+ESCAGSVA_HALLMARK_MITOTIC_SPINDLEEER6.1389e-04-0.2696image
ENSG00000205583.12,STAG3L1ESCAGSVA_HALLMARK_MITOTIC_SPINDLEEAG1.2454e-03-0.2546image
chr7:75367194-75370008:+GBMGSVA_HALLMARK_MYC_TARGETS_V1EER1.2212e-030.2828image
ENSG00000205583.12,STAG3L1GBMGSVA_HALLMARK_MYC_TARGETS_V1EAG1.2306e-030.2826image
ENSG00000205583.12,STAG3L1HNSCGSVA_HALLMARK_SPERMATOGENESISEAG4.0982e-03-0.5168image
chr7:75367194-75370008:+HNSCGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEER3.4013e-03-0.5734image
chr7:75367194-75370008:+KICHGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEER6.3403e-030.3926image
ENSG00000205583.12,STAG3L1KICHGSVA_HALLMARK_OXIDATIVE_PHOSPHORYLATIONEAG3.1319e-030.4220image
ENSG00000205583.12,STAG3L1KIRCGSVA_HALLMARK_PI3K_AKT_MTOR_SIGNALINGEAG1.5086e-04-0.3194image
chr7:75367194-75370008:+KIRCGSVA_HALLMARK_MITOTIC_SPINDLEEER4.2437e-03-0.2492image
chr7:75367194-75370008:+LGGGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEER5.3535e-030.2507image
ENSG00000205583.12,STAG3L1LGGGSVA_HALLMARK_TNFA_SIGNALING_VIA_NFKBEAG4.9384e-030.2433image
ENSG00000205583.12,STAG3L1LIHCGSVA_HALLMARK_MITOTIC_SPINDLEEAG1.2113e-03-0.5317image
chr7:75370646-75371780:+LUADGSVA_HALLMARK_DNA_REPAIREER2.8028e-020.4790image
chr7:75367194-75370008:+LUADGSVA_HALLMARK_PANCREAS_BETA_CELLSEER2.8913e-020.1963image
chr7:75367194-75370008:+OVGSVA_HALLMARK_PANCREAS_BETA_CELLSEER1.3372e-040.2259image
chr7:75386125-75388125:+OVGSVA_HALLMARK_HEDGEHOG_SIGNALINGEER8.4248e-03-0.3651image
ENSG00000205583.12,STAG3L1OVGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG3.5083e-040.2118image
chr7:75370646-75371780:+OVGSVA_HALLMARK_MYC_TARGETS_V1EER3.3059e-030.4765image
chr7:75383043-75384146:+OVGSVA_HALLMARK_PANCREAS_BETA_CELLSEER2.3550e-02-0.4267image
chr7:75367194-75370008:+PAADGSVA_HALLMARK_KRAS_SIGNALING_DNEER1.3786e-020.3962image
ENSG00000205583.12,STAG3L1PAADGSVA_HALLMARK_KRAS_SIGNALING_DNEAG6.1732e-030.4309image
ENSG00000205583.12,STAG3L1PCPGGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG2.9716e-020.2857image
chr7:75367194-75370008:+PCPGGSVA_HALLMARK_PANCREAS_BETA_CELLSEER5.9270e-030.3601image
chr7:75367194-75370008:+PRADGSVA_HALLMARK_UV_RESPONSE_UPEER4.0638e-02-0.1929image
ENSG00000205583.12,STAG3L1PRADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG6.6382e-03-0.2407image
ENSG00000205583.12,STAG3L1SARCGSVA_HALLMARK_BILE_ACID_METABOLISMEAG8.6836e-040.5676image
chr7:75367194-75370008:+SKCMGSVA_HALLMARK_PROTEIN_SECRETIONEER2.3614e-02-0.1751image
chr7:75367194-75370008:+STADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEER9.9908e-070.2694image
ENSG00000205583.12,STAG3L1STADGSVA_HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAYEAG1.7935e-060.2625image
ENSG00000205583.12,STAG3L1TGCTGSVA_HALLMARK_SPERMATOGENESISEAG3.9499e-020.3717image
chr7:75367194-75370008:+TGCTGSVA_HALLMARK_SPERMATOGENESISEER2.1555e-020.4179image
ENSG00000205583.12,STAG3L1THCAGSVA_HALLMARK_DNA_REPAIREAG1.6792e-020.1766image
chr7:75367194-75370008:+THYMGSVA_HALLMARK_P53_PATHWAYEER3.0382e-02-0.2949image


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7. Enriched editing regions and drugs for STAG3L1


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
chr7:75367194-75370008:+BLCADMOGEER5.9643e-03-0.3427image
ENSG00000205583.12,STAG3L1BLCACGP.082996EAG2.8754e-03-0.3587image
ENSG00000205583.12,STAG3L1BRCAGW843682XEAG1.3971e-02-0.1130image
chr7:75367194-75370008:+CESCDMOGEER4.6913e-020.3539image
ENSG00000205583.12,STAG3L1CESCAMG.706EAG9.5313e-03-0.4206image
ENSG00000205583.12,STAG3L1COADLapatinibEAG1.8418e-030.3909image
chr7:75367194-75370008:+COADAS601245EER1.1424e-040.4928image
ENSG00000205583.12,STAG3L1ESCAAZD6244EAG6.4724e-03-0.2158image
chr7:75367194-75370008:+ESCAAICAREER1.0897e-02-0.2021image
chr7:75367194-75370008:+GBMBI.2536EER3.4980e-03-0.2563image
ENSG00000205583.12,STAG3L1GBMBI.2536EAG3.0713e-03-0.2597image
ENSG00000205583.12,STAG3L1HNSCCGP.082996EAG1.7294e-02-0.4387image
chr7:75367194-75370008:+HNSCBicalutamideEER3.7298e-020.4273image
chr7:75367194-75370008:+KICHABT.263EER6.5477e-030.3912image
ENSG00000205583.12,STAG3L1KICHABT.263EAG1.3461e-020.3581image
ENSG00000205583.12,STAG3L1KIRCEmbelinEAG3.1122e-020.1849image
chr7:75367194-75370008:+KIRCJNK.9LEER3.7218e-030.2527image
chr7:75367194-75370008:+KIRPLapatinibEER4.2011e-020.1822image
ENSG00000205583.12,STAG3L1KIRPLenalidomideEAG9.7210e-03-0.2226image
chr7:75367194-75370008:+LAMLDasatinibEER2.3966e-02-0.2213image
ENSG00000205583.12,STAG3L1LAMLDasatinibEAG1.2785e-02-0.2400image
ENSG00000205583.12,STAG3L1LGGA.443654EAG2.1892e-02-0.1994image
chr7:75367194-75370008:+LGGA.443654EER3.9560e-03-0.2591image
ENSG00000205583.12,STAG3L1LIHCKIN001.135EAG4.8514e-050.6384image
ENSG00000205583.12,STAG3L1LUSCGNF.2EAG1.0411e-02-0.2066image
chr7:75367194-75370008:+LUSCGNF.2EER2.3968e-02-0.1894image
chr7:75386125-75388125:+OVBX.795EER1.8446e-030.4257image
chr7:75367194-75370008:+OVLenalidomideEER4.9872e-030.1674image
ENSG00000205583.12,STAG3L1OVJNK.9LEAG2.0322e-030.1833image
chr7:75370646-75371780:+OVCCT007093EER3.2146e-030.4777image
chr7:75383043-75384146:+OVBIBW2992EER1.5944e-02-0.4512image
chr7:75367194-75370008:+PAADCEP.701EER6.5977e-03-0.4332image
ENSG00000205583.12,STAG3L1PAADCEP.701EAG1.7680e-02-0.3780image
chr7:75367194-75370008:+PCPGABT.263EER1.2425e-03-0.4172image
ENSG00000205583.12,STAG3L1PCPGMetforminEAG1.3196e-03-0.4118image
chr7:75367194-75370008:+PRADBAY.61.3606EER2.8575e-04-0.3351image
ENSG00000205583.12,STAG3L1PRADCytarabineEAG9.5027e-05-0.3406image
ENSG00000205583.12,STAG3L1SARCBortezomibEAG2.3601e-02-0.4056image
ENSG00000205583.12,STAG3L1SKCMJW.7.52.1EAG5.3748e-03-0.2044image
chr7:75367194-75370008:+SKCMEmbelinEER1.3621e-030.2458image
ENSG00000205583.12,STAG3L1STADAZ628EAG4.5062e-04-0.1944image
chr7:75367194-75370008:+STADAZ628EER5.8212e-04-0.1913image
ENSG00000205583.12,STAG3L1TGCTBMS.708163EAG3.8883e-02-0.3728image
chr7:75367194-75370008:+TGCTCMKEER4.1553e-02-0.3743image
ENSG00000205583.12,STAG3L1THCAEmbelinEAG1.6594e-020.1769image
ENSG00000205583.12,STAG3L1THYMCyclopamineEAG1.3759e-03-0.4071image
chr7:75367194-75370008:+THYMABT.263EER4.9546e-02-0.2686image
chr7:75367194-75370008:+UCECAICAREER6.9811e-040.6217image
ENSG00000205583.12,STAG3L1UCECMG.132EAG9.7781e-03-0.4433image


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