A prognostic model of 8-T/B cell receptor-related signatures for hepatocellular carcinoma by Xuan Zuo, Hui Li, Shi Xie, Mengfen Shi, Yujuan Guan, Huiyuan Liu, Rong Yan, Anqi Zheng, Xueying Li, Jiabang Liu, Yifan Gan, Haiyan Shi, Keng Chen, Shijie Jia, Guanmei Chen, Min Liao, Zhanhui Wang, Yanyan Han, Baolin Liao

“…Results Finally, an 8-gene prognostic model was successfully established and achieved the validation in both the International Cancer Genome Consortium and Nanfang Hospital cohorts. …”
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Identification of ferroptosis-related signature predicting prognosis and therapeutic responses in pancreatic cancer by Ting Ting Chung, Zanyue Piao, Seung Jin Lee

“…In this study, we developed a prognostic ferroptosis-related gene (FRG)-based risk model using cohorts of The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), proposing plausible therapeutics. …”
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Annotation of Genes Having Candidate Somatic Mutations in Acute Myeloid Leukemia with Whole-Exome Sequencing Using Concept Lattice Analysis by Kye Hwa Lee, Jae Hyeun Lim, Ju Han Kim

“…In cancer genome studies, the annotation of newly detected oncogene/tumor suppressor gene candidates is a challenging process. …”
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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

“…Wilcox test was used to screen the differentially expressed immune-related genes (DEIRGs) in THCA and normal tissues, then the DEIRGs related to prognosis were identified using univariate Cox regression analysis. 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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Analysis of the multigene molecular panel for colorectal cancer in patients under 50 years of age – the preliminary results of the Polish department by Monika Kozłowska-Geller, Piotr Lewitowicz, Monika Wawszczak-Kasza, Łukasz Nawacki, Jarosław Matykiewicz, Stanisław Głuszek

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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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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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IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis by Qi Wang, Xufeng Huang, Shujing Zhou, Yuntao Ding, Huizhi Wang, Weiye Jiang, Min Xu

“…Preliminary analysis of the DEGs was then performed using online gene analysis datasets, such as DAVID, UCSC Cancer Genome Browser, CBioPortal, STRING, and UCSC Cancer Genome Browser. …”
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Solid Predominant Histology and High Podoplanin Expression in Cancer-Associated Fibroblast Predict Primary Resistance to Osimertinib in EGFR-Mutated Lung Adenocarcinoma by Yuji Uehara, MD, Hiroki Izumi, MD, PhD, Tetsuro Taki, MD, PhD, Tetsuya Sakai, MD, PhD, Hibiki Udagawa, MD, PhD, Eri Sugiyama, MD, PhD, Shigeki Umemura, MD, PhD, Yoshitaka Zenke, MD, PhD, Shingo Matsumoto, MD, PhD, Kiyotaka Yoh, MD, PhD, Shoko Kubota, MD, PhD, Keiju Aokage, MD, PhD, Naoya Sakamoto, MD, PhD, Shingo Sakashita, MD, PhD, Motohiro Kojima, MD, PhD, Michiko Nagamine, MD, PhD, Yukio Hosomi, MD, PhD, Masahiro Tsuboi, MD, PhD, Koichi Goto, MD, PhD, Genichiro Ishii, MD, PhD

“…We also investigated HGF mRNA expression levels, using The Cancer Genome Atlas Program and Singapore Oncology Data Portal cohorts. …”
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Deciphering genomic complexity: Understanding intratumor heterogeneity, clonal evolution, and therapeutic vulnerabilities in oral squamous cell carcinoma by Vishnu Priya Veeraraghavan, Bharati R. Doni, Arun Kumar Dasari, Chaitra Patil, Krishna A. Rao, Santosh R. Patil

“…Oral squamous cell carcinoma (OSCC), which is characterized by high rates of recurrence and metastasis, is a prevalent and burdensome form of head and neck cancer. Genomic heterogeneity and clonal evolution play critical roles in OSCC progression and therapeutic resistance. …”
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Alternative Splicing and Its Impact as a Cancer Diagnostic Marker by Yun-Ji Kim, Heui-Soo Kim

“…Furthermore, splicing events occur differently according to cell type, developmental stage, and various diseases, including cancer. Genome instability and flexible proteomes by alternative splicing could affect cancer cells to grow and survive, leading to metastasis. …”
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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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Elucidating the expression and role of cGAS in pan-cancer using integrated bioinformatics and experimental approaches by Zhen Lian, Xue Liu, Xue Li

“…In this study, The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) data were used to analyze the mRNA expression and genomic alterations of cGAS in pan-cancer. …”
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CHST1 as a prognostic-related biomarker in gastric cancer correlating with immune infiltration by Long Gui, Jin-hao Yu, Jia-nan Tan, Guang-yu Zhong, Yong-xue Wang, Lin Zhong, Jiao-jiao Su, Dong Hou, Bin Yang, Fang-hai Han, Sheng-ning Zhou

“…In this study, we obtained the transcriptional profile and corresponding clinical information of CHST1 in gastric cancer (GC) tissues and normal tissues from The Cancer Genome Atlas database. Our functional experiments have demonstrated that CHST1 enhances the proliferation and metastasis of GC cells, both in vitro and in vivo. …”
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Identification and validation of prognostic biomarkers in ccRCC: immune-stromal score and survival prediction by Fang Lyu, Yuxin Zhong, Qingliu He, Wen Xiao, Xiaoping Zhang

“…Methods Data from the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) were subjected to analysis to compute immune and stromal scores utilizing the ESTIMATE algorithm. …”
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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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Construction of a radiogenomic signature based on endoplasmic reticulum stress for predicting prognosis and systemic combination therapy response in hepatocellular carcinoma by Huai-Yu Wu, Shu-Ya Cao, Zheng-Gang Xu, Tian- Wang, Gu-Wei Ji, Ke Wang

“…Methods Using data from The Cancer Genome Atlas Program (TCGA) as a training cohort and data from International cancer genome consortium (ICGC) as a testing cohort. …”
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Titin gene mutations enhance radiotherapy efficacy via modulation of tumour immune microenvironment in rectum adenocarcinoma by Hengchang Liu, Jialiang Liu, Xu Guan, Zhixun Zhao, Pu Cheng, Haipeng Chen, Zheng Jiang, Xishan Wang

“…Methods Data on gene expression and mutations in READ were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. …”
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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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ENTPD8 overexpression enhances anti-PD-L1 therapy in hepatocellular carcinoma via miR-214-5p inhibition by Si-qi Zhao, Min-jie Chen, Fei Chen, Zhao-feng Gao, Xiao-ping Li, Ling-yu Hu, Hai-ying Cheng, Jin-yan Xuan, Jian-guo Fei, Zheng-wei Song

“…Immunohistochemistry, The Cancer Genome Atlas (TCGA) data, and single-cell expression analysis revealed reduced ENTPD8 levels in liver cancer compared to adjacent tissues, with ENTPD8 primarily expressed in tumor cells within the tumor tissue. …”
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