Data analysis of high-throughput sequencing and microarray to identify key signatures of microribonucleic acids in glioblastoma by A. A. Pushkin, E. A. Dzenkova, N. N. Timoshkina, D. Yu. Gvaldin

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Identification of as a Hypermethylated Gene in Colorectal Cancers by Jongbum Kim, Sangsoo Kim

“…We downloaded publicly available DNA methylation and gene expression datasets of matched cancer and normal pairs from the Cancer Genome Atlas Data Portal and performed a systematic computational analysis. …”
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Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer by Dequan Liu, Lei Liu, Xiangyu Che, Guangzhen Wu

“…These genes, which act as tumor suppressors, are referred to as “paradoxical genes.” Analyzing The Cancer Genome Atlas (TCGA) confirmed the widespread presence of paradoxical genes, and KEGG analysis revealed their role in regulating tumor metabolism. …”
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The role of Golgi complex proteins in cell division and consequences of their dysregulation by Roberta Iannitti, Fabiola Mascanzoni, Antonino Colanzi, Daniela Spano

“…Furthermore, TCGA (The Cancer Genome Atlas) database has been queried in order to retrieve information on the genetic alterations and the correlation between the expression of GC-localised proteins and the survival of cancer patients. …”
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Integrative prognostic modeling of ovarian cancer: incorporating genetic, clinical, and immunological markers by Aidi Lin, Feifei Xue, Chenxiang Pan, Lijiao Li

“…Utilizing data from The Cancer Genome Atlas (TCGA), we identified significant prognostic genes through differential expression and survival analysis, integrating these with clinical features and immune landscape assessments including immune cell infiltration and checkpoint expression. …”
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Classification of Genes Based on Age-Related Differential Expression in Breast Cancer by Gunhee Lee, Minho Lee

“…We retrieved the values for gene expression levels in breast cancer and matched normal cells from The Cancer Genome Atlas. We divided genes into two classes by paired t test without considering age in the first classification. …”
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ncRNA-Mediated High Expression of LPCAT1 Correlates with Poor Prognosis and Tumor Immune Infiltration of Liver Hepatocellular Carcinoma by Qiu Sun, Xudong Liu, Qunlong Peng, Lei Hu, Xiaochun Jiang

“…In this study, expression analysis and survival analysis for LPCAT1 in pan cancers were first performed by using The Cancer Genome Atlas (TCGA) data, which suggested that LPCAT1 might be a potential LIHC oncogene. …”
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Correlation between Ferroptosis-Related Gene Signature and Immune Landscape, Prognosis in Breast Cancer by Jiahao Zhu, Qingqing Chen, Ke Gu, You Meng, Shengjun Ji, Yutian Zhao, Bo Yang

“…FRG expression profiles and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO). …”
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tRNA-Uridine Aminocarboxypropyltransferase DTW Domain Containing 2 Suppresses Colon Adenocarcinoma Progression by Yun Qian, Yu-Jiang Li, Yi-Wei Fu, Cui-Xia Liu, Juan Wang, Bin Yang

“…We first evaluated the transcription and mRNA levels of DTWD2 using data from The Cancer Genome Atlas. Besides, we tested its mRNA and protein expression in our enrolled retrospective cohort. …”
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An Investigation of the Prognostic Role of Genes Related to Lipid Metabolism in Head and Neck Squamous Cell Carcinoma by Ling Qian, Chenyu Zhou, Keyi Wang, Liuyang Li, Wenhui Xia, Yuan Fan

“…A prognostic risk model composed of eight differentially expressed LMRGs (PHYH, CYP4F8, INMT, ELOVL6, PLPP3, BCHE, TPTE, and STAR) was constructed through The Cancer Genome Atlas database. Then, ELOVL6 expression was validated in oral squamous cell carcinoma (OSCC), which is a common type of HNSCC, by immunohistochemical analysis. …”
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Integrins identified as potential prognostic markers in osteosarcoma through multi-omics and multi-dataset analysis by Lei Cui, Shuai Zhao, Hai long Teng, Biao Yang, Qian Liu, An Qin

“…The IRS’s utility in predicting overall survival was confirmed using data from The Cancer Genome Atlas, underscoring its potential in personalized cancer management.…”
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Identification of the Immune Cell Infiltration Landscape in Head and Neck Squamous Cell Carcinoma (HNSC) for the Exploration of Immunotherapy and Prognosis by Chunli Huang, Jifeng Liu

“…An analysis of the Cancer Genome Atlas (TCGA) database revealed gene expression profiles and corresponding clinical information. …”
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The Theranostic Genome by Xiaoying Xu, Pablo Jané, Vincent Taelman, Eduardo Jané, Rebecca A. Dumont, Yonathan Garama, Francisco Kim, María del Val Gómez, Karim Gariani, Martin A. Walter

“…Using a deep learning-based hybrid human-AI pipeline that cross-references PubMed, the Gene Expression Omnibus, DisGeNET, The Cancer Genome Atlas and the NIH Molecular Imaging and Contrast Agent Database, we bridge individual genes in human cancers with respective theranostic compounds. …”
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Validation of histopathology foundation models through whole slide image retrieval by Saghir Alfasly, Ghazal Alabtah, Sobhan Hemati, Krishna Rani Kalari, Joaquin J. Garcia, H. R. Tizhoosh

“…Our experiments were conducted on diagnostic slides from The Cancer Genome Atlas (TCGA), which covers 23 organs and 117 cancer subtypes. …”
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Intratumoral microbiota, fatty acid metabolism, and tumor microenvironment constitute an unresolved trinity in colon adenocarcinoma by Guangyi Liu, Kun Liu, Lei Ji, Yang Li

“…Here, we analyzed intratumoral microbiome samples and matched host transcriptome samples from 420 patients with COAD in The Cancer Genome Atlas (TCGA). All patients were divided into two subtypes (FAM_high and FAM_low) based on the Gene set variation analysis (GSVA) score of FAM pathway. …”
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Brain gliomas new transcriptomic discoveries from differentially expressed genes to therapeutic targets by Shiwen Pei, Zhiquan Jiang, Hongwei Cheng

“…Gene set enrichment analysis and immunocytometric analysis further explored the biological functions and pathways of identified genes, which were validated using The Cancer Genome Atlas and Genotype-Tissue Expression datasets. …”
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A Novel 8-Gene Prognostic Signature for Survival Prediction of Uveal Melanoma by Zhongjun Tang, Kebo Cai

“…In the validation phase, the signature was validated in The Cancer Genome Atlas database. Results. Forty-one genes were identified as hub genes of metastasis by WGCNA. …”
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ERRα promotes glycolytic metabolism and targets the NLRP3/caspase-1/GSDMD pathway to regulate pyroptosis in endometrial cancer by Pingping Su, Xiaodan Mao, Jincheng Ma, Lixiang Huang, Lirui Yu, Shuting Tang, Mingzhi Zhuang, Zhonglei Lu, Kelvin Stefan Osafo, Yuan Ren, Xinrui Wang, Xite Lin, Leyi Huang, Xiaoli Huang, Elena Ioana Braicu, Jalid Sehouli, Pengming Sun

“…In addition, the expression of ERRα-related pyroptosis genes was analyzed using The Cancer Genome Atlas and Gene Expression Omnibus database. …”
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Multidimensional Analysis of PANoptosis-Related Molecule CASP8: Prognostic Significance, Immune Microenvironment Effect, and Therapeutic Implications in Hepatocellular Carcinoma by Fei Peng, Fang Zhu, Baodi Cao, Liang Peng

“…We conducted a comprehensive analysis using public data from the Cancer Genome Atlas, Human Protein Atlas, Tumor Immune Single Cell Hub, and STRING databases. …”
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Multiple programmed cell death patterns predict the prognosis and drug sensitivity in gastric cancer by Qiying Song, Shihe Liu, Di Wu, Aizhen Cai

“…The diverse patterns of programmed cell death (PCD) are significantly associated with the pathogenesis and progression of GC, and it has the potential to serve as prognostic and drug sensitivity indicators for GC.MethodThe sequencing data and clinical characteristics of GC patients were downloaded from The Cancer Genome Atlas and GEO databases. LASSO cox regression method was used to screen feature genes and develop the PCD score (PCDS). …”
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