Comprehensive analysis of the expression and prognostic value of ARMCs in pancreatic adenocarcinoma by Guanxiang Zhuo, Shengzhai Lin, Fei Yuan, Qiaoling Zheng, Yinpin Guo, Zuwei Wang, Jianfei Hu, Meihong Yao, Fuxiu Zhong, Shi Chen, Yanling Chen, Huixing Chen

“…Methods We used the The Cancer Genome Atlas (TCGA) database for survival analysis. …”
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Targeting HVEM-GPT2 axis: a novel approach to T cell activation and metabolic reprogramming in non-small cell lung cancer therapy by Yuanshan Yao, Chunji Chen, Bin Li, Wen Gao

“…Methods The lung cancer datasets for this study were directly downloaded from The Cancer Genome Atlas (TCGA). Single-cell data were sourced from the Tumor Immune Single-cell Hub (TISCH). …”
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TUBA1B as a novel prognostic biomarker correlated with immunosuppressive tumor microenvironment and immunotherapy response by Juntao Qi, Juntao Qi, Mingming Zhou, Na Yang, Huiyun Ma, Min He, Gujie Wu, Chang Ge, Liuyin Jin, Lin Cheng, Wei Liao, Hefei Ren, Caiyun Lei

“…Despite its fundamental roles, TUBA1B’s impact on tumor prognosis and the tumor immune microenvironment across cancer types remains inadequately understood.Methods To elucidate TUBA1B’s role in cancer prognosis and immune response, we conducted a comprehensive analysis, integrating data from established databases such as The Cancer Genome Atlas, Genotype Tissue Expression, Cancer Cell Lineage Encyclopedia, Human Protein Atlas, Kaplan-Meier Plotter, cBioPortal, TIMER, and ImmuCellAI, along with a large-scale clinical study and immunotherapy cohort. …”
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Identification of Potential lncRNAs and miRNAs as Diagnostic Biomarkers for Papillary Thyroid Carcinoma Based on Machine Learning by Fei Yang, Jie Zhang, Baokun Li, Zhijun Zhao, Yan Liu, Zhen Zhao, Shanghua Jing, Guiying Wang

“…The data of lncRNA, miRNA, and mRNA were downloaded from the Cancer Genome Atlas (TCGA) dataset, followed by functional analysis of differentially expressed mRNAs. …”
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A Novel Immune-Related lncRNA-Based Model for Survival Prediction in Clear Cell Renal Cell Carcinoma by Zedan Zhang, Yanlin Tang, Yanjun Liu, Hongkai Zhuang, Enyu Lin, Lu Xie, Xiaoqiang Feng, Kaiwen Tian, Jiayi Zeng, Jiumin Liu, Yuming Yu

“…The transcription profile and clinical information were obtained from The Cancer Genome Atlas (TCGA). Immune-related gene sets and transcription factor genes were downloaded from GSEA website and Cistrome database, respectively. …”
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Integrating single-cell RNA-Seq and bulk RNA-Seq data to explore the key role of fatty acid metabolism in hepatocellular carcinoma by Hua Dai, Xin Tao, Yuansen Shu, Fanrong Liu, Xiaoping Cheng, Xiushen Li, Bairui Shu, Hongcheng Luo, XuXiang Chen, Zhaorui Cheng

“…Data procurement encompassed transcriptomic and clinical datasets from HCC patients, sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) repositories. …”
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Lactate Dehydrogenase-A-Forming LDH5 Promotes Breast Cancer Progression by Fang T, Hu L, Chen T, Li F, Yang L, Liang B, Wang W, Zeng F

“…We aimed to explore the roles of LDHA and LDH5 isoenzyme activity in BC, which provides a new insight into LDHA for the treatment of BC.Methods: The expression of LDHA in BC and its relationship with clinicopathological features were obtained from various databases including The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), Breast Cancer-Gene Expression Miner (bc-GenExMiner), TNMplot, UALCAN. …”
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Multiomic characterization, immunological and prognostic potential of SMAD3 in pan-cancer and validation in LIHC by Tao Zhou, Dan Dan Zhang, Jiejing jin, Jinyang Xie, Jianhua Yu, Chao Zhu, Rong Wan

“…We extensively harnessed data from authoritative sources, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), cBioPortal, Human Protein Atlas (HPA), UALCAN, and various other databases. …”
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MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy by Gaofeng Ni, Yuwei Sun, Hongling Jia, Zhikai Xiahou, Yumeng Li, Fu Zhao, Hongyan Zang

“…Methods: The study utilized single-cell RNA sequencing (scRNA-seq) data sourced from the Gene Expression Omnibus database and The Cancer Genome Atlas to analyze HR+BC and identify key cellular characteristics. …”
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Unveiling the role of ASPP1 in cancer progression: pan-cancer bioinformatics and experimental validation in colorectal cancer by Keyuan Xiao, Xiang Li, Ihsan Ullah, Wenqing Hu, Kaiqiang Wang, Fan Yang, Chengyu Yang, Chunqi Feng, Liang Zong, Xinghua Li

“…Data were extracted from public resources, including The Cancer Genome Atlas (TCGA), GTEx, and the Human Protein Atlas, and analyzed via tools such as cBioPortal, GEPIA, and TIMER2. …”
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EHMT2‐mediated R‐loop formation promotes the malignant progression of prostate cancer via activating Aurora B by Yuyang Zhang, Mingqin Su, Yiming Chen, Li Cui, Wei Xia, Renfang Xu, Dong Xue, Xiansheng Zhang, Xingliang Feng

“…Methods Bioinformatic analyses were conducted to identify genes overexpressed in PCa tissues using The Cancer Genome Atlas (TCGA) and GEO datasets. Western blotting and immunohistochemistry assays were applied to determine the expression levels of euchromatic histone lysine methyltransferase 2 (EHMT2), pT232‐Aurora B and Cullin 3 (CUL3). …”
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CASC8 activates the pentose phosphate pathway to inhibit disulfidptosis in pancreatic ductal adenocarcinoma though the c-Myc-GLUT1 axis by Hong-Fei Yao, Jieqiong Ge, Jiahao Chen, Xiaoyan Tang, Chunjing Li, Xiao Hu, Abousalam Abdoulkader Ahmed, Yunlong Pu, Guihua Zhou, Tongyi Zhang, Zhiwei Cai, Chongyi Jiang

“…CASC8 expression and its clinical correlations were analyzed using data from The Cancer Genome Atlas (TCGA) and further verified by chromogenic in situ hybridization assay in PDAC tissues. …”
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Integrating single-cell RNA-seq and bulk RNA-seq to explore prognostic value and immune landscapes of methionine metabolism-related signature in breast cancer by Yanxian Gao, Ziyu Feng, Hailong Zhao, Xinghai Liu, Muyu Zhu, Xiafei Yu, Xiaoan Liu, Xian Wu, Jing Tao

“…Breast cancer cell lines have been identified as methionine-dependent, and methionine restriction has been proposed as a potential cancer treatment strategy.MethodsWe integrated transcriptomic and single-cell RNA sequencing (ScRNA-seq) analyses based on The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. …”
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Differential impact of TIM-3 ligands on NK cell function by Xin Zhang, Lazar Vujanovic, Riyue Bao, Robert L Ferris, Tullia C Bruno, Aditi Kulkarni, Hridesh Banerjee, Housaiyin Li, Juncheng Wang, Lawrence P Kane, Pragati Upadhyay, Jennifer L Anderson, Onyedikachi Victor Onyekachi, Lidia M R B Arantes

“…In vitro killing, proliferation and cytokine production assays were implemented to evaluate whether the four TIM-3 ligands differentially modulate TIM-3+ NK cell functions, and whether disruption of TIM-3/ligand interaction can enhance NK cell-mediated antitumor effector mechanisms. Finally, The Cancer Genome Atlas survival analysis and digital spatial profiling were employed to study the potential impact of etiology-associated differences on patients with HNSCC outcomes.Results We demonstrate that TIM-3 is highly prevalent on circulating and tumor-infiltrating NK cells. …”
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Upregulated SAE1 Drives Tumorigenesis and Is Associated with Poor Clinical Outcomes in Breast Cancer by Hong Liu, Jing Wang, Yunhai Li, Feng Luo, Lei Xing

“…Bioinformatics analysis was applied to analyze SAE1 expression in BC and normal breast tissues, its relationship with clinicopathologic characteristics and prognosis in BC patients, and data from the Cancer Genome Atlas database and Gene Expression Omnibus dataset. …”
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Identification of a 5-Gene-Based Scoring System by WGCNA and LASSO to Predict Prognosis for Rectal Cancer Patients by He Huang, Shilei Xu, Aidong Chen, Fen Li, Jiezhong Wu, Xusheng Tu, Kunpeng Hu

“…Sequencing (or microarray) data and clinicopathological details of patients with RC were retrieved from The Cancer Genome Atlas (TCGA-READ) or the Gene Expression Omnibus (GSE123390, GSE56699) database. …”
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Spatial transcriptomics reveals unique metabolic profile and key oncogenic regulators of cervical squamous cell carcinoma by Limin Zhou, Jiejie Liu, Peipei Yao, Xing Liu, Fei Chen, Yu Chen, Li Zhou, Chao Shen, You Zhou, Xin Du, Junbo Hu

“…We also employed The Cancer Genome Atlas (TCGA) database to examine the analysis results of ST data. …”
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The lysosome-related characteristics affects the prognosis and tumor microenvironment of lung adenocarcinoma by Wuguang Chang, Wuyou Gao, Yawei Wu, Bin Luo, Lekai Zhong, Leqi Zhong, Wenqian Lin, Zhesheng Wen, Youfang Chen

“…However, there are few studies on lysosome-associated genes (LAGs) in lung adenocarcinoma (LUAD).MethodsBulk RNA-seq of LUAD was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). …”
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Glioma Image-Level and Slide-Level Gene Predictor (GLISP) for Molecular Diagnosis and Predicting Genetic Events of Adult Diffuse Glioma by Minh-Khang Le, Masataka Kawai, Kenta Masui, Takashi Komori, Takakazu Kawamata, Yoshihiro Muragaki, Tomohiro Inoue, Ippei Tahara, Kazunari Kasai, Tetsuo Kondo

“…In this study, the Cancer Genome Atlas whole-slide images (WSIs) were used to train the model. …”
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A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer by Veronica Rendo, Michael Schubert, Nicholas Khuu, Maria F. Suarez Peredo Rodriguez, Declan Whyte, Xiao Ling, Anouk van den Brink, Kaimeng Huang, Michelle Swift, Yizhou He, Johanna Zerbib, Ross Smith, Jonne Raaijmakers, Pratiti Bandopadhayay, Lillian M. Guenther, Justin H. Hwang, Amanda Iniguez, Susan Moody, Ji-Heui Seo, Elizabeth H. Stover, Levi Garraway, William C. Hahn, Kimberly Stegmaier, René H. Medema, Dipanjan Chowdhury, Maria Colomé-Tatché, Uri Ben-David, Rameen Beroukhim, Floris Foijer

“…We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. …”
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