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Editing gene: NMD3 (ImmuneEditome ID:51068) |
1. Gene summary of enriched editing regions for NMD3 |
 Gene summary |
| Gene information | Gene symbol | NMD3 | Gene ID | 51068 | ||||||||||||
| GeneSynonyms | CGI-07 | |||||||||||||||
| GeneCytomap | 3q26.1 | |||||||||||||||
| GeneType | protein-coding | |||||||||||||||
| GeneDescription | 60S ribosomal export protein NMD3|NMD3 homolog|hNMD3 | |||||||||||||||
| GeneModificationdate | 20230517 | |||||||||||||||
| UniprotID | Q96D46;C9J0B9;C9JA08;C9K0C2;C9IZW9;C9IY70 | |||||||||||||||
| PubMed ID |
| UCSC image. |
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| Locations of each EERs. |
| EER | ENST | ENSG | GeneName | Region | Repeat | dsRNA structure |
| chr3:161111714-161111940:+ | ENST00000460503.4 | ENSG00000169251.11 | NMD3 | intronic | MSTA,L1MCa | chr3:161111714-161111940:+.alignment |
| chr3:161111714-161111940:+ | ENST00000468606.4 | ENSG00000169251.11 | NMD3 | intronic | MSTA,L1MCa | chr3:161111714-161111940:+.alignment |
| chr3:161115012-161115286:+ | ENST00000460503.4 | ENSG00000169251.11 | NMD3 | intronic | MSTA | chr3:161115012-161115286:+.alignment |
| chr3:161115012-161115286:+ | ENST00000468606.4 | ENSG00000169251.11 | NMD3 | intronic | MSTA | chr3:161115012-161115286:+.alignment |
| chr3:161128651-161130077:+ | ENST00000460503.4 | ENSG00000169251.11 | NMD3 | intronic | AluSx1,AluJr,L1MC5a,L1MB3 | chr3:161128651-161130077:+.alignment |
| chr3:161128651-161130077:+ | ENST00000468606.4 | ENSG00000169251.11 | NMD3 | intronic | AluSx1,AluJr,L1MC5a,L1MB3 | chr3:161128651-161130077:+.alignment |
| chr3:161197829-161198018:+ | ENST00000460503.4 | ENSG00000169251.11 | NMD3 | intronic | AluJr4 | chr3:161197829-161198018:+.alignment |
| chr3:161197829-161198018:+ | ENST00000468606.4 | ENSG00000169251.11 | NMD3 | intronic | AluJr4 | chr3:161197829-161198018:+.alignment |
| chr3:161201126-161201721:+ | ENST00000460503.4 | ENSG00000169251.11 | NMD3 | intronic | (ATT)n,AluSx,AluSx1 | chr3:161201126-161201721:+.alignment |
| chr3:161201126-161201721:+ | ENST00000468606.4 | ENSG00000169251.11 | NMD3 | intronic | (ATT)n,AluSx,AluSx1 | chr3:161201126-161201721:+.alignment |
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2. Tumor-specific enriched editing regions for NMD3 |
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| Comparison of enriched editing regions between tumor and normal. |
| * P<0.05 and Informative number >=20. |
| * EER: enriched editing region, EAG: EER-associated genes. |
| ID_events | cancer | Type | P | Boxplot |
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| Correlation 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_events | cancer | Type | StageType | AnovaP | P | R | Boxplot |
| chr3:161201126-161201721:+ | BRCA | Path | EER | 4.9075e-02 | 1.3857e-02 | -0.4856 |  |
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| Associations of enriched editing regions with cancer survival. |
| * Pkm<0.05 and Pcox<0.05. |
| * EER: enriched editing region, EAG: EER-associated genes. |
| ID_events | cancer | TypeID | Pkm | Pcox_continuous | HR_continuous | KMPlot |
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3. Enriched editing regions and immune related genes for NMD3 |
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| 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_events | cancer | Type | Gene | beta | FDR | PearsonP | PearsonR | CorrelationPlot | RBP | RBPtargets | ImmuneGene | ImmuneFraction | HallMark |
More results |
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4. Enriched editing regions and immune related splicing for NMD3 |
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| 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_events | cancer | Type | SplicingType | SplicingGene | SplicingChr | SplicingPosition | beta | FDR | PearsonP | PearsonR | CorrelationPlot | RBP | RBPtargets | ImmuneGene | ImmuneFraction | HallMark |
More results |
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5. Enriched editing regions and immune infiltration for NMD3 |
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| 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_events | cancer | TypeID | ImmuneCell | P | R | CorrelationPlot |
| chr3:161111714-161111940:+ | BLCA | EER | NK_cells_resting | 5.9300e-03 | 0.5344 |  |
| ENSG00000169251.11,NMD3 | BLCA | EAG | NK_cells_resting | 2.2169e-03 | 0.5541 |  |
| chr3:161111714-161111940:+ | BRCA | EER | Dendritic_cells_activated | 8.3019e-03 | 0.3847 |  |
| ENSG00000169251.11,NMD3 | STAD | EAG | T_cells_CD4_memory_activated | 2.3255e-02 | 0.3113 |  |
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6. Enriched editing regions and immune gene sets for NMD3 |
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| 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_events | cancer | Type | E2M_P | Boxplot | CorP | CorR | CorrelationPlot |
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| 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_events | cancer | Type | Buffa_P | Buffa_R | Ragnum_P | Ragnum_R | Winter_P | Winter_R | HALLMARK_P | HALLMARK_R | CorrelationPlot |
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| 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_events | cancer | HallmarkType | Type | P | R | CorrelationPlot |
| chr3:161201126-161201721:+ | BRCA | GSVA_HALLMARK_UV_RESPONSE_UP | EER | 1.7262e-03 | 0.6052 |  |
| ENSG00000169251.11,NMD3 | BRCA | GSVA_HALLMARK_INTERFERON_ALPHA_RESPONSE | EAG | 4.6456e-02 | 0.2406 |  |
| chr3:161111714-161111940:+ | ESCA | GSVA_HALLMARK_P53_PATHWAY | EER | 3.0434e-02 | 0.3195 |  |
| ENSG00000169251.11,NMD3 | ESCA | GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS | EAG | 1.8908e-02 | 0.3309 |  |
| ENSG00000169251.11,NMD3 | GBM | GSVA_HALLMARK_TGF_BETA_SIGNALING | EAG | 2.2378e-02 | 0.4300 |  |
| ENSG00000169251.11,NMD3 | OV | GSVA_HALLMARK_HEDGEHOG_SIGNALING | EAG | 2.0707e-02 | -0.1888 |  |
| chr3:161111714-161111940:+ | OV | GSVA_HALLMARK_KRAS_SIGNALING_DN | EER | 1.6083e-02 | -0.2053 |  |
| chr3:161111714-161111940:+ | STAD | GSVA_HALLMARK_CHOLESTEROL_HOMEOSTASIS | EER | 3.4460e-02 | 0.3692 |  |
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7. Enriched editing regions and drugs for NMD3 |
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| 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_events | cancer | Drug | Type | P | R | CorrelationPlot |
| chr3:161111714-161111940:+ | BLCA | LFM.A13 | EER | 1.3705e-02 | 0.4863 |  |
| ENSG00000169251.11,NMD3 | BLCA | LFM.A13 | EAG | 1.7053e-02 | 0.4471 |  |
| chr3:161201126-161201721:+ | BRCA | Docetaxel | EER | 2.2053e-02 | -0.4650 |  |
| ENSG00000169251.11,NMD3 | BRCA | Cisplatin | EAG | 4.1787e-02 | -0.2458 |  |
| chr3:161111714-161111940:+ | ESCA | CHIR.99021 | EER | 5.5342e-03 | -0.4026 |  |
| ENSG00000169251.11,NMD3 | ESCA | CHIR.99021 | EAG | 1.5694e-02 | -0.3400 |  |
| chr3:161201126-161201721:+ | KIRC | BIBW2992 | EER | 3.2296e-02 | 0.4380 |  |
| ENSG00000169251.11,NMD3 | OV | JNK.9L | EAG | 3.7101e-03 | 0.2356 |  |
| chr3:161111714-161111940:+ | OV | CMK | EER | 1.8475e-03 | 0.2637 |  |
| ENSG00000169251.11,NMD3 | STAD | AICAR | EAG | 4.7152e-02 | 0.2739 |  |
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| EAGs targeted by drugs from DrugBank database. |
| * EAG: EER-associated genes. |
| EER | ENST | UniprotID | DrugBankID | Drug | DrugType |
