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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A Micro-RNA Connection in BRafV600E-Mediated Premature Senescence of Human Melanocytes by Gang Ren, Jingwei Feng, Ila Datar, Aaron H. Yeung, Srinivas Vinod Saladi, Yongqing Feng, Ivana de la Serna, Kam C. Yeung

“…Recent high-throughput-sequencing of the cancer genome has identified oncogenic mutations in BRaf genetic locus as one of the critical events in melanomagenesis. …”
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Comprehensive Cellular Senescence Evaluation to Aid Targeted Therapies by Xiaolan Zhou, Xiaofeng Zhu, Weixu Wang, Jing Wang, Haimei Wen, Yuqi Zhao, Jiayu Zhang, Qiushi Xu, Zhaozhao Zhao, Ting Ni

“…We quantified the cellular senescence states of ~10,000 tumor samples from The Cancer Genome Atlas and examined their associations with targeted drug responses. …”
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Loss of Lkb1 cooperates with BrafV600E and ultraviolet radiation, increasing melanoma multiplicity and neural‐like dedifferentiation by Kimberley McGrail, Elena González‐Sánchez, Paula Granado‐Martínez, Roberto Orsenigo, Yuxin Ding, Berta Ferrer, Javier Hernández‐Losa, Iván Ortega, Juan Martín‐Caballero, Eva Muñoz‐Couselo, Vicente García‐Patos, Juan A. Recio

“…Analysis of human melanoma tumors [data from The Cancer Genome Atlas (TCGA)] revealed that 50% or more of the samples expressed no or low amounts of serine/threonine protein kinase STK11 (also known as LKB1) protein. …”
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Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in color... by Xiaoyu Qin, Wenjuan Xu, Jinxiu Wu, Ming Li

“…We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. …”
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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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GPX8 as a Novel Prognostic Factor and Potential Therapeutic Target in Primary Glioma by Zhao-shou Yang, Qin Yang, Xiao-xiao Sun, Kui Xiong, Xiao-ting Zhu, Yi-chen Wang, Qian-yao Ren, Guo-hui Wu, Shi-min Wang, Xu-qin Cao, Xiao-rong Yang, Wen-gong Jiang

“…Here, we leveraged Chinese Glioma Genome Atlas (CGGA), The Cancer Genome Atlas (TCGA), and Genotype-Tissue Expression (GTEx) database to investigate the association between GPX8 and overall survival (OS) of patients with primary gliomas, and our results showed that GPX8 expression was negatively correlated with OS. …”
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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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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

“…Our previous research demonstrated that NP could promote the proliferation and epithelial-mesenchymal transition (EMT) of colorectal cancer (CRC) cells; however, the specific mechanism remains unclear. miRNA sequencing revealed that NP upregulated the expression levels of microRNA(miR)-151a-3p in CRC. Analysis of The Cancer Genome Atlas (TCGA) data revealed increased expression levels of miR-151a-3p in CRC tissues. …”
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Expressional Subpopulation of Cancers Determined by G64, a Co-regulated Module by Jae-Woong Min, Sun Shim Choi

“…RNA sequencing-based transcriptome data derived from 22 cancers, except LADC, were downloaded from The Cancer Genome Atlas (TCGA). Interestingly, the 22 cancers also expressed the G64 genes in a correlated manner, as observed previously in an LADC study. …”
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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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Widespread mutagenesis and chromosomal instability shape somatic genomes in systemic sclerosis by Sriram Vijayraghavan, Thomas Blouin, James McCollum, Latarsha Porcher, François Virard, Jiri Zavadil, Carol Feghali-Bostwick, Natalie Saini

“…In the genomes of patients with systemic sclerosis, we find evidence of somatic hypermutation or kategis (typically only seen in cancer genomes), we identify mutation signatures closely resembling the error-prone translesion polymerase Polη activity, and observe an activation-induced deaminase-like mutation signature, which overlaps with genomic regions displaying kataegis.…”
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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 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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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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Impact of frequent ARID1A mutations on protein stability provides insights into cancer pathogenesis by Rajen K. Goutam, Gangtong Huang, Exequiel Medina, Feng Ding, William J. Edenfield, Hugo Sanabria

“…We analyzed five frequent missense mutations R1020S, M1022K, K1047Q, G1063V, and A1089T identified in The Cancer Genome Atlas (TCGA) to assess their effects on the stability of the ARID domain using a hybrid experimental and computational approach. …”
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Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System by Chundi Gao, Huayao Li, Wenzhe Ma, Qiming Zhang, Cun Liu, Lijuan Liu, Jing Zhuang, Changgang Sun

“…We systematically studied correlations among important M6A methylation regulators, tumor mutational burden (TMB), and immune infiltration in clinical and sequencing data from the LUAD cohort of the cancer genome map (TCGA). The molecular subtype clusters 1 and 2 were identified by the consensus clustering of 16 M6A regulatory factors. …”
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Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma by Fan Yang, Xiaodong Jia, Zihuan Ma, Siyao Liu, Chunzi Liu, Dan Chen, Xiuju Wang, Niansong Qian, Hui Ma

“…LUSC patient data from The Cancer Genome Atlas (TCGA), including microbial genus level abundance data and RNA sequencing (RNA-Seq) data, were used as a training dataset. …”
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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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