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Kruppel-family zinc finger proteins as emerging epigenetic biomarkers in head and neck squamous cell carcinoma
Published 2023-05-01“…Methods We examined prognostic significance of ZNF154 and ZNF132 expression and DNA methylation in independent patient cohort of about 500 head and neck cancer patients in the Cancer Genome Atlas (TCGA). We also overexpressed these genes in HEK-293 cells, as well as the oral cancer cell line UM-SCC-1. …”
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503
DNA methylation of ACADS promotes immunogenic cell death in hepatocellular carcinoma
Published 2025-01-01“…Methods and results Using RNA sequencing data from different tumours in The Cancer Genome Atlas database, we observed that ACADS was downregulated and hypermethylated in HCC. …”
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504
RETRACTED ARTICLE: Single-cell omics and machine learning integration to develop a polyamine metabolism-based risk score model in breast cancer patients
Published 2024-10-01“…Data from The Cancer Genome Atlas, Gene Expression Omnibus, and Genotype-Tissue Expression identified 286 differentially expressed genes linked to polyamine pathways in breast cancer. …”
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505
MicroRNA-150-3p enhances the antitumour effects of CGP57380 and is associated with a favourable prognosis in non-small cell lung cancer
Published 2025-01-01“…A similar analysis was performed using data from The Cancer Genome Atlas (TCGA). Cell proliferation, colony formation and migration assays were validated in A549 and H157 cells treated with miR-150-3p mimics. …”
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The immune-related gene CD5 is a prognostic biomarker associated with the tumor microenvironment of breast cancer
Published 2025-01-01“…In this study, we obtained the RNA-seq data of 1086 patients from The Cancer Genome Atlas (TCGA) database. We calculated the proportions of tumor-infiltrating immune cells (TICs) and immune and stromal components using the CIBERSORT and ESTIMATE methods, and we screened differentially expressed genes (DEGs). …”
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507
Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma
Published 2025-02-01“…LUSC patient data from The Cancer Genome Atlas (TCGA), including microbial genus level abundance data and RNA sequencing (RNA-Seq) data, were used as a training dataset. …”
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Prognostic value of FCER1G expression and M2 macrophage infiltration in esophageal squamous cell carcinoma
Published 2025-02-01“…Methods The expression of FCER1G and its prognostic value in ESCC was examined by The Cancer Genome Atlas and Gene Expression Omnibus databases. We also evaluated the relationship between FCER1G expression and 22 TIICs. …”
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Combining extracellular matrix proteome and phosphoproteome of chickpea and meta‐analysis reveal novel proteoforms and evolutionary significance of clade‐specific wall‐associated e...
Published 2024-03-01“…We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta‐analyses of 74 plant matrisomes. …”
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Integrating multiomics analysis and machine learning to refine the molecular subtyping and prognostic analysis of stomach adenocarcinoma
Published 2025-01-01“…We downloaded the multiomics data of STAD patients in The Cancer Genome Atlas (TCGA)-STAD cohort, which included mRNA, microRNA, long non-coding RNA, somatic mutation, and DNA methylation data, from the sxdyc website. …”
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Критичний аналіз гелієвих газобалонних систем наддування паливних баків ракетних двигунів
Published 2023-06-01“…Достатньо навести як приклад РРД РН «Зеніт», «Циклон-4М, «Маяк» (Україна), Antares (США та Україна), Atlas-V, Falcon 9 (США), "Чанчжен-7" та "Чанчжен-9 (КНР), КSLV-I, КSLV-II (Південна Корея) та ін. …”
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In-depth characterization of miRNome in papillary thyroid cancer with BRAF V600E mutation
Published 2020-03-01“…MiRNAs differentially expressed between BRAF V600E-positive and BRAF V600E-negative PTC tissues were validated in silico using The Cancer Genome Atlas (TCGA) THCA datasets containing 420 samples. …”
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The Identification and Validation of a Robust Immune-Associated Gene Signature in Cutaneous Melanoma
Published 2021-01-01“…Methods. 434 melanoma patients were extracted from The Cancer Genome Atlas (TCGA) database, and 1811 IAGs were downloaded from the ImmPort database in our retrospective study. …”
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Identification of Ferroptosis-Associated Long Noncoding RNA Prognostic Model and Tumor Immune Microenvironment in Thyroid Cancer
Published 2022-01-01“…The TC lncRNA data were extracted from RNA sequencing files of The Cancer Genome Atlas (TCGA). Then, we performed a two-cluster analysis and grouped 502 patients with TC in a 7 : 3 ratio. …”
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Macrophages Phenotype Regulated by IL-6 Are Associated with the Prognosis of Platinum-Resistant Serous Ovarian Cancer: Integrated Analysis of Clinical Trial and Omics
Published 2023-01-01“…We used ESTIMATE to calculate the number of immune and stromal components in high-grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas database. The differential expression genes (DEGs) were analyzed via protein–protein interaction network, Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis to reveal major pathways of DEGs. …”
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Transcriptomic analysis of Medicago truncatula calli with MtWOX9-1 overexpression
Published 2019-10-01“…Using Medicago Truncatula Gene Expression Atlas, we also identified a group of genes coding for transcription factors that were both coexpressed with MtWOX9-1 in different plant organs and differentially expressed in our samples. …”
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Relationship between inherited genetic variation and survival from colorectal cancer stratified by tumour location
Published 2025-01-01“…We investigated the relationship between Phosphatidylinositol 4-Kinase Type 2 Beta (PI4K2B) expression in colorectal tumours and survival in 597 patients from The Human Protein Atlas (THPA). We also analysed 3 SNPs previously associated with survival by anatomical site. …”
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Prognostic Significance and Therapeutic Potential of SERPINE1 in Head and Neck Squamous Cell Carcinoma
Published 2025-01-01“…Methods and Results In this study, we delved into the variations in gene mutation, methylation patterns, and expression levels of SERPINE1 in head and neck squamous cell carcinoma (HNSCC) and normal tissues, leveraging comprehensive analyses of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. …”
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A Narrative Review of Prognostic Gene Signatures in Oral Squamous Cell Carcinoma Using LASSO Cox Regression
Published 2025-01-01“…It is essential to distinguish between cancers arising in the head and neck regions due to significant differences in their etiologies, treatment approaches, and prognoses. As the Cancer Genome Atlas (TCGA) dataset is available in HNSCC, the survival analysis prognosis of OSCC patients based on the TCGA dataset for discovering gene expression-based prognostic biomarkers is limited. …”
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A Novel Prognostic Signature Revealed the Interaction of Immune Cells in Tumor Microenvironment Based on Single-Cell RNA Sequencing for Lung Adenocarcinoma
Published 2022-01-01“…The bioinformatics data of LUAD patients could be approached from The Cancer Genome Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) analyses were performed to construct a risk model. …”
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