Exploring salivary gene expression clusters: A bioinformatics approach for advanced diagnosis and prognosis in head and neck squamous cell carcinoma by Rajesh Parsanathan, Rishaba Byju, D.S. Prabakaran

“…Materials and methods: A comprehensive keyword search was conducted to extract 74 salivary gland secretion genes from the Human Protein Atlas. GeneMANIA and STRING databases were employed to analyse protein-protein interactions and predict functional partners. …”
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Intersection of rare pathogenic variants from TCGA in the All of Us Research Program v6 by Blaine A. Bates, Kylee E. Bates, Spencer A. Boris, Colin Wessman, David Stone, Justin Bryan, Mary F. Davis, Matthew H. Bailey

“…Summary: Using rare cancer predisposition alleles derived from The Cancer Genome Atlas (TCGA) and high cancer prevalence (14% of participants) in All of Us (version 6), we assessed the impact of these rare alleles on cancer occurrence in six broad groups of genetic similarity provided by All of Us: African/African American (AFR), Admixed American/Latino (AMR), East Asian (EAS), European (EUR), Middle Eastern (MID), or South Asian (SAS). …”
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Novel protein-based prognostic signature linked to immunotherapeutic efficiency in ovarian cancer by Shuo-Fu Chen, Liang-Yun Wang, Yi-Sian Lin, Cho-Yi Chen

“…Methods The workflow was demonstrated based on the Reverse Phase Protein Array (RPPA) and RNA-sequencing profiles of ovarian cancer patients from The Cancer Genome Atlas (TCGA). The algorithm began by clustering patients using immune-related gene sets, which allowed us to identify immune-related proteins of interest. …”
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Dwarf Galaxies with Radio-excess Active Galactic Nuclei in the Very Large Array Sky Survey by John-Michael Eberhard, Amy E. Reines, Hansung B. Gim, Jeremy Darling, Jenny E. Greene

“…We find a 2 σ threshold of q < 1.94 to select radio-excess AGNs, which is derived from a sample of ∼7000 galaxies across the full mass range in the NASA-Sloan Atlas that have radio and IR detections from VLASS and the Wide-Field Infrared Survey Explorer, respectively. …”
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Immune gene features and prognosis in colorectal cancer: insights from ssGSEA typing by Anwen Huang, Jinxiu Wu, Jiakuan Wang, Chengwen Jiao, Yunfei Yang, Huaiwen Xiao, Li Yao

“…Methods We obtained and merged RNA-Seq data along with clinical details for colorectal cancer (CRC) from The Cancer Genome Atlas (TCGA) repository, and then performed immunocluster typing on all CRC specimens. …”
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Facilitators and barriers affecting the implementation of e-health for chronic respiratory diseases in remote settings: a qualitative evidence synthesis by Emil Matias Salmi, Francesca Wanda Basile, Faiz Ahmad Khan, Larry Watt, Rinn Song, Else Margreet Bijker

“…Findings were coded with Atlas.ti software and categorised based on an adapted Digital Health Equity Framework. …”
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Single-cell RNA-seq analysis reveals microenvironmental infiltration of myeloid cells and pancreatic prognostic markers in PDAC by Yanying Fan, Lili Wu, Xinyu Qiu, Han Shi, Longhang Wu, Juan Lin, Jie Lin, Tianhong Teng

“…Methods Single-cell RNA sequencing (scRNA-seq) data were downloaded from t the Tumor Immune Single-cell Hub and gene expression data were retrieved from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. …”
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Weakly supervised deep learning-based classification for histopathology of gliomas: a single center experience by Mingrong Zuo, Xiang Xing, Linmao Zheng, Hao Wang, Yunbo Yuan, Siliang Chen, Tianping Yu, ShuXin Zhang, Yuan Yang, Qing Mao, Yongbin Yu, Ni Chen, Yanhui Liu

“…We analyzed 472 whole slide images (WSIs) from 226 patients in West China Hospital (WCH) and 1604 WSIs from 880 patients in The Cancer Genome Atlas (TCGA). We utilized the OpenSlide library to load WSIs, segmented them into small patches using the DeepZoom module, and then normalized the color using the Reinhard method. …”
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UBE2J1 is identified as a novel plasma cell-related gene involved in the prognosis of high-grade serous ovarian cancer by Yunjie Tian, Ruoyu Dong, Yingxia Guan, Ying Wang, Wei Zhao, Jun Zhang, Shan Kang

“…The effects of immune cell markers on prognosis were analyzed via univariate Cox regression, least absolute shrinkage and selection operator (LASSO) and gene set variation analysis (GSVA) of bulk sequencing data from The Cancer Genome Atlas (TCGA)-HGSOC cohort. Finally, the effects of key markers on HGSOC cells were evaluated via Cell Counting Kit-8 (CCK-8), Transwell, colony formation, wound healing, immunofluorescence and in vivo tumor growth assays. …”
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Screening and validation of tsRNAs associated with lung adenocarcinoma by LU Chunli, SHAN Yifan, XIE Weijia

“…The effects of tsRNAs expression levels on the prognosis of lung adenocarcinoma patients were analyzed based on the Cancer Genome Atlas （TCGA） database （TCGA-LUAD）. The target genes were predicted based on TRFtarget2.0 and tRFTar databases. …”
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Analysing DNA methylation and transcriptomic signatures to predict prostate cancer recurrence risk by Fahad M. Aldakheel, Hadeel Alnajran, Shatha A. Alduraywish, Ayesha Mateen, Mohammed S. Alqahtani, Rabbani Syed

“…This study employs a machine learning approach to identify DNA methylation and RNA expression biomarkers predictive of PCa recurrence using datasets from The Cancer Genome Atlas (TCGA). We analyzed 49,133 genes, identifying 684 differentially methylated genes (DMGs) and 691 differentially expressed genes (DEGs) between recurrence and non-recurrence groups. …”
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Exploration of the Immune-Related Signatures and Immune Infiltration Analysis in Melanoma by Ai-lan Li, Yong-mei Zhu, Lai-qiang Gao, Shu-yue Wei, Ming-tao Wang, Qiang Ma, You-you Zheng, Jian-hua Li, Qing-feng Wang

“…The transcriptome profiling and clinical data of melanoma were downloaded from The Cancer Genome Atlas database, and their matched normal samples were obtained from the Genotype-Tissue Expression database. …”
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Feasibility of implementing family-integrated newborn care for hospitalised preterm and low birthweight infants in newborn care units of Ethiopia: a mixed-methods design by Hege Langli Ersdal, Araya Abrha Medhanyie, Damen Haile Mariam, Siren Rettedal, Znabu Hadush Kahsay

“…Despite the WHO’s call for family engagement in newborn care, evidence of the feasibility of implementation remains scarce.Design An observational feasibility study employing a mixed-methods design comprising a quantitative cross-sectional survey among 157 healthcare providers (HCPs) and a qualitative Participatory Rural Appraisal.Setting The study was conducted in 30 neonatal care units (NCUs) of hospitals in Tigray, Northern Ethiopia.Participants HCPs who were on duty in NCUs during the data collection period were included in the study.Analysis Descriptive statistics were obtained for the quantitative data using STATA V.16, while qualitative data were coded and analysed using a framework analysis approach with qualitative data analysis software (Atlas.ti V.9).Results In total, 157 HCPs were enrolled with a mean (SD) age of 32 (±6.8) years. …”
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Mapping Drug-Resistant Tuberculosis Treatment Outcomes in Hunan Province, China by Temesgen Yihunie Akalu, Archie C. A. Clements, Zuhui Xu, Liqiong Bai, Kefyalew Addis Alene

“…Sociodemographic, economic, healthcare, and environmental variables were obtained from various sources, including the WorldClim database, the Malaria Atlas Project, and the Hunan Bureau of Statistics. …”
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Deciphering the heterogeneity and plasticity of the tumor microenvironment in liver cancer provides insights for prognosis by Yihao Sun, Yihao Sun, Guojuan Shi, Jian Yang, Chun-Zhong Zhou, Chuhan Peng, Yu-Hong Luo, Ying Pan, Rui-Qi Wang

“…Using genomic and clinical data from The Cancer Genome Atlas, we identified specific cell components linked to tumor characteristics and genetics. …”
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Development and experimental validation of dephosphorylation-related biomarkers to assess prognosis and immunotherapeutic response in gliomas by Hui Tang, Xuping Yang, Xuping Yang, Guoqian Li, Ke Peng, Yang Sun, Longyang Jiang, Longyang Jiang, Yilan Huang, Yilan Huang

“…This study aims to construct a validated prognostic risk model for dephosphorylation, which will provide new directions for clinical treatment, prognostic assessment, and temozolomide (TMZ) resistance in glioma patients.MethodsScreening dephosphorylation-related genes (DRGs) and transcriptome expression data from The Cancer Genome Atlas (TCGA), Molecular signatures database (MSigDB) and constructing risk scoring models. …”
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The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research by Ashkan Kalantary-Charvadeh, Saman Morovat, Somayeh Aslani, Nasrin Ziamajidi, Amirnader Emami Razavi, Roghayeh Abbasalipourkabir

“…Using The Cancer Genome Atlas, we analyzed lncRNA, miRNA, and mRNA sequencing data for OSCC. …”
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RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…Method mRNA (messenger RNA) data and clinical records pertaining to colon cancer were retrieved from The Cancer Genome Atlas (TCGA) database. The analysis of NR3C2 expression discrepancies between normal colon and tumor tissues was conducted using R software. …”
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Comprehensive Analysis of Competing Endogenous RNA Network Focusing on Long Noncoding RNA Involved in Cirrhotic Hepatocellular Carcinoma by Yuli Zhang, Dinggui Chen, Miaomiao Yang, Xianfeng Qian, Chunmei Long, Zhongwei Zheng

“…The lncRNA, miRNA, and mRNA expression datasets were obtained from Gene Expression Omnibus and The Cancer Genome Atlas. Based on miRanda and TargetScan, the HCC-specific ceRNA network was constructed to illustrate the coexpression regulatory relationship of lncRNAs, miRNAs, and mRNAs. …”
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Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma by Rui Mu, Yuehong Shen, Chuanbin Guo, Xinyun Zhang, Hongyu Yang, Huijun Yang

“…Finally, the hub gene’s differential mRNA expression levels were evaluated by means of the Gene Expression Profiling Interactive Analysis (GEPIA), and the Human Protein Atlas (HPA) was utilized for the validation of their translational levels. …”
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