Matrix Metalloproteinase-9 is associated with tumor microenvironment remodeling of bladder cancer by Fang Fang, Tiange Wu, Mengxue Wang, Wenchao Li, Zonghao You, Ming Chen, Han Guan

“…We utilized these two algorithms to analyze the immune components of 433 bladder cancer cases from The Cancer Genome Atlas database, aiming to compensate for the current lack of large-sample single-cell information. …”
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Correcting scale distortion in RNA sequencing data by Christopher Thron, Farhad Jafari

“…We examined several RNA-seq datasets from the Cancer Genome Atlas (TCGA), Stand Up 2 Cancer (SU2C), and GTEx databases with various types of preprocessing. …”
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Impact of Extracellular Matrix-Related Genes on the Tumor Microenvironment and Prognostic Indicators in Esophageal Cancer: A Comprehensive Analytical Study by Yinghong Wu, Wenjie Hu, Zhihong Jia, Qiying Zhu, Jinghui Xu, Liang Peng, Renjie Wang

“…Our study utilized next-generation sequencing and clinical data from esophageal cancer patients provided by The Cancer Genome Atlas, employing the R package in RStudio for computational analysis. …”
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Integrative bioinformatics and immunohistochemical analysis unravel the prognostic significance and immunological implication of LIMCH1 in breast cancer: a retrospective study by Xin Yu, Bei Li, Wenge Li, Jingping Yuan, Shengrong Sun, Juanjuan Li

“…This study employed an integrative approach combining bioinformatics analysis of The Cancer Genome Atlas (TCGA) cohort and clinical immunohistochemistry (IHC) cohort data. …”
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Construction of a 12-gene prognostic model for colorectal cancer based on heat shock protein-related genes by Qin Tong, Junchao Zhou

“…Transcriptional data and clinical information of CRC patients were obtained from The Cancer Genome Atlas (TCGA) database, and a literature search was conducted to identify HSP-related genes. …”
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Identification and Validation of a Potential Stemness-Associated Biomarker in Hepatocellular Carcinoma by Yangyang Zhang, Ruike Zhang, Lingxiu Zeng, Haizhou Wang, Ruyi Peng, Meng Zhang, Hailin Zhang, Zhenwei Yang, Liping Gao, Meng Wang, Jing Liu

“…The data of HCC patients from The Cancer Genome Atlas (TCGA) were collected and divided based on the mRNA expression-based stemness index (mRNAsi) in this study. …”
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Identification of a Novel PPAR Signature for Predicting Prognosis, Immune Microenvironment, and Chemotherapy Response in Bladder Cancer by Ke Zhu, Wen Deng, Hui Deng, Xiaoqiang Liu, Gongxian Wang, Bin Fu

“…The RNA sequencing data and clinical information of BLCA patients were acquired from The Cancer Genome Atlas (TCGA). The differentially expressed PPAR-targeted genes were investigated. …”
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A Systematic Pan-Cancer Analysis of YY1 Aberrations and their Relationship with Clinical Outcome, Tumor Microenvironment, and Therapeutic Targets by Xinghao Fu, Feihong Ji, Qi He, Xinguang Qiu

“…We first explored the potential carcinogenic effect of YY1 in 33 cancers using the cancer genome atlas (TCGA) project and gene expression omnibus (GEO) datasets in this research. …”
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Landscape of Alternative Splicing Events Related to Prognosis and Immune Infiltration in Glioma: A Data Analysis and Basic Verification by Hong-xin Su, Gang Yang, Fei Su, Chen-xiao Hu, Tao Zhang, Jun-tao Ran, Quan-lin Guan

“…RNA splicing patterns were collected from The Cancer Genome Atlas SpliceSeq database, followed by calculating the percentage of splicing index. …”
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Nonylphenol promotes epithelial-mesenchymal transition in colorectal cancer cells by upregulating miR-151a-3p by Biao Wang, Nianjie Zhang, Lin Dai, Yuanwei Zhang, Shuo Yin, Xuefeng Yang

“…Analysis of The Cancer Genome Atlas (TCGA) data revealed increased expression levels of miR-151a-3p in CRC tissues. …”
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CTSK and PLAU as Prognostic Biomarker and Related to Immune Infiltration in Pancreatic Cancer: Evidence from Bioinformatics Analysis and qPCR by Yuntao Ding, Zhangzuo Li, Huizhi Wang, Qi Wang, Han Jiang, Zhengyue Yu, Min Xu

“…Expression profiles and clinical data from the Cancer Genome Atlas (TCGA) were then used to compare the expression levels of CTSK and PLAU in pancreatic cancer and healthy pancreatic tissues via the Wilcoxon rank-sum test, with further validation using qPCR. …”
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Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma by Mengmeng Hua, Tao Li

“…LRG mRNA and long non-coding RNA transcriptomes, epigenetic methylation data, and somatic mutation data from The Cancer Genome Atlas LUAD cohort were analyzed to identify lactylation cancer subtypes (CSs) using 10 multiomics ensemble clustering techniques. …”
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Exploring Unique Extracellular Vesicles Associated Signatures: Prognostic Insights, Immune Microenvironment Dynamics, and Therapeutic Responses in Pancreatic Adenocarcinoma by Kai Nan, Ming Zhang, Zilong Geng, Yuankai Zhang, Lin Liu, Zhi Yang, Peng Xu

“…Initially, we identified differentially expressed lncRNAs (DELs) from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project datasets. …”
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Mining Prognostic Biomarkers of Thyroid Cancer Patients Based on the Immune-Related Genes and Development of a Reliable Prognostic Risk Model by Hongjun Fei, Xu Han, Yanlin Wang, Shuyuan Li

“…According to The Cancer Genome Atlas (TCGA) cohort, we developed a least absolute shrinkage and selection operator (LASSO) regression prognostic model and performed validation analyses regard to the predictive value of the model in internal (TCGA) and external (International Cancer Genome Consortium) cohorts respectively. …”
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Unveiling the role of SYNGR4 in breast cancer development: a novel target for immunotherapy by Jie Ma, Hongtao Wang, Zhengwei Gui, Yuanrong Yang

“…IntroductionSYNGR4 is considered to be one of the causative genes for amyotrophic lateral sclerosis, but its role in breast cancer development has not been revealed.MethodsThe expression of SYNGR4 in a variety of malignancies including breast cancer was analyzed using Genotype Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) databases and verified by specimens collected from our center. …”
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Somatic Mutaome Profile in Human Cancer Tissues by Nayoung Kim, Yourae Hong, Doyoung Kwon, Sukjoon Yoon

“…Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. …”
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AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs by Samuel S. Boyd, Chad Slawson, Jeffrey A. Thompson

“…AMEND was applied to two real-world multi-omic datasets: renal cell carcinoma data from The cancer genome atlas and an O-GlcNAc Transferase knockout study. …”
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HAVCR1 Affects the MEK/ERK Pathway in Gastric Adenocarcinomas and Influences Tumor Progression and Patient Outcome by Ji Xue, Ying Li, Jianfeng Yi, Hong Jiang

“…We first determined the expression of HAVCR1 in GAC tissues compared with normal gastric tissues based on the Cancer Genome Atlas (TCGA) database using bioinformatics analysis methods. …”
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Identification of the circRNA-miRNA-mRNA Regulatory Network in Bladder Cancer by Bioinformatics Analysis by Jiancheng Lv, Ping-an Chang, Xin Li, Xiao Yang, Jie Han, Hao Yu, Zijian Zhou, Haiwei Yang, Pengchao Li, Jiexiu Zhang, Qiang Lu

“…We obtained four datasets of circRNA, microRNA (miRNA), and messenger (mRNA) expression profiles from the Gene Expression Omnibus and The Cancer Genome Atlas microarray databases and identified 434, 367, and 4799/4841 differentially expressed circRNAs, miRNAs, and mRNAs, respectively. …”
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Exploring PANoptosis in head and neck cancer: A novel approach to cancer therapy by Li Wang, Baisheng Lin, Feixiang Wang, Zili Dai, Guofeng Xie, Jian Zhang

“…This study utilises transcriptomic and clinical data related to HNSC from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. …”
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