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541
A Metabolic Gene Signature to Predict Overall Survival in Head and Neck Squamous Cell Carcinoma
Published 2020-01-01“…In this study, we used RNA sequencing (RNA-seq) data from the cancer genome atlas (TCGA), with validation in the GEO dataset to profile the metabolic microenvironment and define potential biomarkers for metabolic therapy. …”
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542
Impact of rare non-coding variants on human diseases through alternative polyadenylation outliers
Published 2025-01-01“…Here we constructed a comprehensive atlas of alternative polyadenylation (APA) outliers (aOutliers), including 1334 3′ UTR and 200 intronic aOutliers, from 15,201 samples across 49 human tissues. …”
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543
Integrating RNA-seq and scRNA-seq to explore the prognostic features and immune landscape of exosome-related genes in breast cancer metastasis
Published 2025-12-01“…Objective This study aims to explore the role of exosome-related genes in breast cancer (BRCA) metastasis by integrating RNA-seq and single-cell RNA-seq (scRNA-seq) data from BRCA samples and to develop a reliable prognostic model.Methods Initially, a comprehensive analysis was conducted on exosome-related genes from the BRCA cohort in The Cancer Genome Atlas (TCGA) database. Three prognostic genes (JUP, CAPZA1 and ARVCF) were identified through univariate Cox regression and Lasso-Cox regression analyses, and a metastasis-related risk score model was established based on these genes. …”
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544
The heterogeneity of NOTCH1 to tumor immune infiltration in pan-cancer
Published 2024-11-01“…In this study, the data originated from the Genotype-Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) databases were input into multiple online bioinformatic tools to study the characteristics of NOTCH1 in pan-cancer. …”
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545
NIPAL1 as a prognostic biomarker associated with pancreatic adenocarcinoma progression and immune infiltration
Published 2025-01-01“…Primitive RNA sequencing (RNA-seq) data of PAAD from The Cancer Genome Atlas (TCGA) was utilized for bioinformatics analysis to characterize the expression levels of NIPAL1 in tumor and normal tissues. …”
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546
Genome wide identification of Dof transcription factors in Carmine radish reveals RsDof33 role in cadmium stress and anthocyanin biosynthesis
Published 2025-02-01“…Cd stress-induced RsDof expression patterns were studied using an RNA-seq atlas and qRT-PCR. The majority of RsDofs were tissue-specific and Cd-sensitive. …”
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547
The Use of Machine Learning to Create a Risk Score to Predict Survival in Patients with Hepatocellular Carcinoma: A TCGA Cohort Analysis
Published 2021-01-01“…Methods. The Cancer Genome Atlas (TCGA-LIHC) was analyzed for differentially expressed genes. …”
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548
Cell-free supernatants from plant growth-promoting rhizobacteria Bacillus albus strains control Aspergillus flavus disease in peanut and maize seedlings
Published 2025-01-01“…These were characterized using rapid chemical assays and ultra-high-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight/mass spectrometry (UHPLC-ESI-QTOF/MS), combined with bioinformatic tools such as Global Natural Product Social Molecular Networking (GNPS) and Natural Products Atlas (NPAtlas). Identified putative antifungal compounds included two diketopiperazines (cyclo(Pro-Leu) and cyclo(2-hydroxy-Pro-Leu)), four macrolactins (7-O-succinyl macrolactin A, 7-O-methyl-5′-hydroxy-3′-heptenoate-macrolactin, macrolactin B, and macrolactin C), two siderophores (petrobactin and bacillibactin), and three cyclic lipopeptides (kurstakin 1, 2 or 3, and 4). …”
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549
Elevated POSTN expression predicts poor prognosis and is associated with radioresistance in cervical cancer patients treated with radical radiotherapy
Published 2025-02-01“…We analyzed data from 92 CC patients in The Cancer Genome Atlas (TCGA) and 153 patients from our institution, assessing POSTN expression levels through mRNA analysis and immunohistochemistry (IHC). …”
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550
Gestão do conhecimento em instituições de ensino superior: um estudo na Universidade Federal Rural do Semiárido
Published 2025-01-01“…Para análise dos dados foi utilizada a técnica de análise de conteúdo, e a exploração e codificação do material foi realizada por meio do software ATLAS.TI. Com base nas análises foi possível identificar as dificuldades vivenciadas pelos servidores quando mudam de setor, tais como: inexistência de compilado normativo, dificuldades em entender a rotina em virtude da ausência de ferramenta de consulta, rotinas integralmente tácitas, dentre outros. …”
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551
Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection
Published 2020-01-01“…We identified differentially expressed microRNAs (DEMs) and genes (DEGs) from the Gene Expression Omnibus (GEO) dataset, constructed microRNA-(miRNA-)mRNA expression networks, analyzed the function and signal pathway of cross-genes, analyzed the relations between cross-genes and GC prognosis with the Cancer Genome Atlas (TCGA) data, and verified the expression of cross-genes in patients with H. pylori infection. …”
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552
Prognostic values of intracellular cell-related genes in esophageal cancer and their regulatory mechanisms
Published 2025-01-01“…Hence, investigating the prognostic significance and regulatory mechanisms of genes related to these intracellular structures in esophageal cancer is imperative. The Cancer Genome Atlas (TCGA) Esophageal Cancer (ESCA) dataset served as the training set for the analysis. …”
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553
Bright night sleeping environment induces diabetes and impaired glucose tolerance in non-human primates
Published 2025-02-01“…BackgroundAccording to the IDF Diabetes Atlas regularly published by International Diabetes Federation, the prevalence of diabetes and impaired glucose tolerance (IGT), diabetes-related mortality and health expenditure are becoming serious eventually at the global, regional and national level. …”
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554
Population Kinetics and Protein Profiles of Co-Cultured Adult and Fetus Rabbit Bladder Smooth Muscle Cells
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555
Promising markers of CIMP+ colon tumors identified on the basis of TCGA data analysis
Published 2018-01-01“…For the identification of CpG sites, the methylation level of which could be used to detect CIMP+ tumors, an analysis of expression and methylation profiles of 297 primary colon tumors and 38 histologically normal tissues paired to them, which are presented in the TCGA (The Cancer Genome Atlas) project database, was performed by us using the CrossHub tool created previously. …”
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556
Identification of critical biomarkers and immune landscape patterns in glioma based on multi-database
Published 2025-01-01“…Patients and methods Differentially expressed genes (DEGs) of glioma were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. …”
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557
Developing and validating a drug recommendation system based on tumor microenvironment and drug fingerprint
Published 2025-01-01“…Clinical application was assessed using The Cancer Genome Atlas (TCGA) dataset, with Best Overall Response (BOR) serving as the clinical efficacy measure. …”
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558
Key regions aberrantly connected within cerebello-thalamo-cortical circuit and their genetic mechanism in schizophrenia: an fMRI meta-analysis and transcriptome study
Published 2025-01-01“…Gene annotation analysis was performed to identify genes over-expressed in these regions by using the Allen Human Brain Atlas, followed by a set of gene functional feature analyses. 19 studies (1333 patients and 1174 healthy controls) were included in this meta-analysis. …”
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559
Potential biomarkers and immune infiltration linking endometriosis with recurrent pregnancy loss based on bioinformatics and machine learning
Published 2025-02-01“…Moreover, immune cell infiltration was estimated using CIBERSORTx, and the Cancer Genome Atlas (TCGA) database was employed to elucidate the role of key genes in endometrial carcinoma (EC).Results26 common differentially expressed genes (DEGs) were screened in both diseases, three of which were identified as common core genes (MAN2A1, PAPSS1, RIBC2) through the combination of WGCNA, PPI network, and machine learning-based feature selection. …”
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560
Single-cell sequencing uncovers the mechanistic role of DAPK1 in glioma and its diagnostic and prognostic implications
Published 2025-01-01“…However, the precise role and underlying mechanisms of DAPK1 in gliomas remain inadequately understood.MethodsWe performed analyses on RNA-seq and microarray datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), in addition to single-cell RNA sequencing (scRNA-seq) data from glioma patients available in GEO. …”
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