The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research by Ashkan Kalantary-Charvadeh, Saman Morovat, Somayeh Aslani, Nasrin Ziamajidi, Amirnader Emami Razavi, Roghayeh Abbasalipourkabir

“…Abstract This study explores the role of LINC00839 and its potential interaction with the miR-195-5p/cyclin E1 (CCNE1) axis in oral squamous cell carcinoma (OSCC). Using The Cancer Genome Atlas, we analyzed lncRNA, miRNA, and mRNA sequencing data for OSCC. …”
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RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…Method mRNA (messenger RNA) data and clinical records pertaining to colon cancer were retrieved from The Cancer Genome Atlas (TCGA) database. The analysis of NR3C2 expression discrepancies between normal colon and tumor tissues was conducted using R software. …”
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Comprehensive Analysis of Competing Endogenous RNA Network Focusing on Long Noncoding RNA Involved in Cirrhotic Hepatocellular Carcinoma by Yuli Zhang, Dinggui Chen, Miaomiao Yang, Xianfeng Qian, Chunmei Long, Zhongwei Zheng

“…The lncRNA, miRNA, and mRNA expression datasets were obtained from Gene Expression Omnibus and The Cancer Genome Atlas. Based on miRanda and TargetScan, the HCC-specific ceRNA network was constructed to illustrate the coexpression regulatory relationship of lncRNAs, miRNAs, and mRNAs. …”
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Identification and Verification of Novel Biomarkers Involving Rheumatoid Arthritis with Multimachine Learning Algorithms: An In Silicon and In Vivo Study by Fucun Liu, Juelan Ye, Shouli Wang, Yang Li, Yuhang Yang, Jianru Xiao, Aimin Jiang, Xuhua Lu, Yunli Zhu

“…We retrieved RA-related and pan-cancer information datasets from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. Six gene expression profiles and corresponding clinical information of GSE12021, GSE29746, GSE55235, GSE55457, GSE77298, and GSE89408 were adopted to perform differential expression gene analysis, enrichment, and immune component difference analyses of RA. …”
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Prognostic models of immune-related cell death and stress unveil mechanisms driving macrophage phenotypic evolution in colorectal cancer by Hao Liu, Chuhan Zhang, Sanfei Peng, Yuhan Yin, Yishi Xu, Sihan Wu, Liping Wang, Yang Fu

“…Furthermore, we performed enrichment analyses and deconvolution algorithms to elucidate the complex interactions between immune cell infiltration and the processes of PCD and stress within a substantial array of transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data base (GEO) related to CRC. …”
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Identification of Five m6A-Related lncRNA Genes as Prognostic Markers for Endometrial Cancer Based on TCGA Database by Li Shan, Ye Lu, Cheng-Cheng Xiang, Xiaoli Zhu, Er-Dong Zuo, Xu Cheng

“…Gene expression and clinical data were extracted from The Cancer Genome Atlas. Coexpression analysis was performed to identify m6A-related lncRNAs, which were entered into univariate Cox regression models for evaluating the prognosis of UCEC. …”
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Identification of HOXA9 methylation as an epigenetic biomarker predicting prognosis and guiding treatment choice in acute myeloid leukemia by Fei Xie, Ting-juan Zhang, Xin-long Zhang, Zi-jun Xu, Liang Qiao, Yun Wang, Yang-jing Zhao, Jun Qian, Jing-dong Zhou

“…Methods We systematically first screened the prognostic value of HOXA cluster genes methylation in AML from The Cancer Genome Atlas (TCGA) datasets. Afterwards, the candidate prognosis-related gene HOXA9 were selected for clinical relevance analysis and were further validated in another independent cohort from our research center. …”
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Knockdown of NDUFAF6 inhibits breast cancer progression via promoting mitophagy and apoptosis by Shang Wu, Xindi Ma, Xiangmei Zhang, Kaiye Du, Chao Shi, Ahmed Ali Almaamari, Boye Han, Suwen Su, Yunjiang Liu

“…Background While NDUFAF6 is implicated in breast cancer, its specific role remains unclear.Methods The expression levels and prognostic significance of NDUFAF6 in breast cancer were assessed using The Cancer Genome Atlas, Gene Expression Omnibus, Kaplan-Meier plotter and cBio-Portal databases. …”
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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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Revisiting ABC Transporters and Their Clinical Significance in Glioblastoma by Brandon Wee Siang Phon, Shalini Sundramurthi Chelliah, Dina El-Rabie Osman, Saatheeyavaane Bhuvanendran, Ammu Kutty Radhakrishnan, Muhamad Noor Alfarizal Kamarudin

“…Using the datasets in The Cancer Genome Atlas and Gene Expression Omnibus, we found upregulated ABC transporters that either negatively impacted survival in univariate analyses (ABCA1, ABCA13, ABCB9, ABCD4) or were independent negative prognosis factors for patients with GBM (ABCA13, ABCB9). …”
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Downregulated mRNA Expression of ZNF385B Is an Independent Predictor of Breast Cancer by Ning Yan, Cong Liu, Fang Tian, Ling Wang, Yimin Wang, Zhaoying Yang, Yan Jiao, Miao He

“…Furthermore, data of patients with BC were downloaded from The Cancer Genome Atlas (TCGA). The receiver operating characteristic (ROC) curve of ZNF385B expression was established to explore the diagnostic value of ZNF385B and to obtain the cut-off value of high or low ZNF385B expression in BC. …”
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SUMO modified ETV1 promotes M2-polarized tumor-associated macrophage infiltration and cancer progression by facilitating CCL2 transcription in esophageal squamous cell carcinoma ce... by Tianci Han, Xiaoqi Guo, Junwei Xie, Wei Tong, Liang Zhang

“…Methods Gene expression and immune infiltration in ESCC samples from the Cancer Genome Atlas (TCGA) were analyzed. The expression of ETV1 in clinical samples was detected by real-time PCR, western blot and immunohistochemistry staining. …”
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Therapeutic target genes and regulatory networks of gallic acid in cervical cancer by Zhixi You, Ye Lei, Yongkang Yang, Zhihui Zhou, Xu Chao, Keyi Ju, Songyi Wang, Yuanyuan Li, Yuanyuan Li

“…By combining the results of the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) analysis and RNA-seq, the differentially expressed genes (DEGs), including those upregulated and downregulated genes in CC compared with the normal cervix in the GEO and TCGA database, while expressed reversed after treatment with GA, were identified. …”
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TOM40 as a prognostic oncogene for oral squamous cell carcinoma prognosis by Lifei Deng, Hong Ran, Dunhui Yang, Zhen Wang, Peng Zhao, Hengjie Huang, Yongjin Wu, Peng Zhang

“…Methods TOM40 expression level in OSCC was evaluated using datasets downloaded from The Cancer Genome Atlas (TCGA), as well as clinical data. The correlation between TOM40 expression level and the clinicopathological parameters and survival were analyzed in TCGA. …”
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CST2 promotes cell proliferation and regulates cell cycle by activating Wnt-β-catenin signalling pathway in serous ovarian cancer by Xiaohua Wang, Sufen Zhao, Yanwei Guo, Chunhui Wang, Shuyu Han, Xingcha Wang

“…Therefore, we aimed to investigate the expression levels, survival outcomes, immune cell infiltration, proliferation, cell cycle, and underlying molecular mechanisms associated with the CST2 signature in SOC.Methods The Cancer Genome Atlas database was used to acquire clinical information and CST2 expression profiles from patients with SOC. …”
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Identification of SETD4 as an Onco‐Immunological Biomarker Encompassing the Tumor Microenvironment, Prognoses, and Therapeutic Responses in Various Human Cancers by Yuyun Zhong, Ruiqi Wang, Zijie Huang, Zhaoting Hu, Bin Peng, Bin Chen, Liyue Sun

“…Methods Utilizing The Cancer Genome Atlas database, and other publicly accessible platforms, we comprehensively analyzed SETD4 gene expression, methylation patterns, and prognostic significance. …”
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SHP2 promotes the epithelial-mesenchymal transition in triple negative breast cancer cells by regulating β-catenin by Shihan Qian, Jingjing Zhu, Qing Han, Huang Cheng, Huaibin Zhou

“…Methods In this study, we conducted bioinformatics analysis of the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases to examine PTPN11 (encoding SHP2) expression levels and perform survival analysis in TNBC. …”
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DOCK4 Is a Platinum-Chemosensitive and Prognostic-Related Biomarker in Ovarian Cancer by Qianqian Zhao, Jie Zhong, Ping Lu, Xiao Feng, Ying Han, Chenqi Ling, Wenke Guo, Weijin Zhou, Fudong Yu

“…The gene expression profiles were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. A total of 4 genes (AP2A2, DOCK4, HSDL2, and PDK4) were the candidate differentially expressed genes (DEGs) of PPAR-TRGs with platinum chemosensitivity. …”
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A disintegrin and metallopeptidase domain (ADAM) 12, ADAM 17 mRNA and ADAM10 protein hold potential as biomarkers for detection of early gastric cancer by Sooyeon Oh, Sang-Soo Lee, Hoeyoung Jin, Seo-Hyeon Choi, Choong-Keun Cha, Jooho Lee, KyuBum Kwack, Sang Gyun Kim, Sang-Woon Choi

“…As a proof-of-concept pilot study, the expression of ADAM8, ADAM9, ADAM10, ADAM12, ADAM17, and major histocompatibility complex (MHC) class I chain-related sequence A (MICA), a ligand for NKG2D, in gastric cancer was investigated in silico using The Cancer Genome Atlas (TCGA) database. Subsequently, the mRNA and protein expression levels of these markers except ADAM8 were tested in blood samples from patients with EGC and healthy controls. …”
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Construction and validation of prognosis and treatment outcome models based on plasma membrane tension characteristics in bladder cancer by Zhipeng Wang, Sheng Li, Fuchun Zheng, Situ Xiong, Lei Zhang, Liangwei Wan, Chen Wang, Xiaoqiang Liu, Jun Deng

“…Methods Transcriptomic, clinical and mutation data from BLCA patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. …”
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