RETRACTED ARTICLE: Single-cell omics and machine learning integration to develop a polyamine metabolism-based risk score model in breast cancer patients by Xiliang Zhang, Hanjie Guo, Xiaolong Li, Wei Tao, Xiaoqing Ma, Yuxing Zhang, Weidong Xiao

“…Data from The Cancer Genome Atlas, Gene Expression Omnibus, and Genotype-Tissue Expression identified 286 differentially expressed genes linked to polyamine pathways in breast cancer. …”
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MicroRNA-150-3p enhances the antitumour effects of CGP57380 and is associated with a favourable prognosis in non-small cell lung cancer by Hongmei Zheng, Songqing Fan, Jiadi Luo, Qiuyuan Wen, Hongjing Zang

“…A similar analysis was performed using data from The Cancer Genome Atlas (TCGA). Cell proliferation, colony formation and migration assays were validated in A549 and H157 cells treated with miR-150-3p mimics. …”
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The immune-related gene CD5 is a prognostic biomarker associated with the tumor microenvironment of breast cancer by Yi Zhao, Hengheng Zhang, Wenwen Wang, Guoshuang Shen, Miaozhou Wang, Zhen Liu, Jiuda Zhao, Jinming Li

“…In this study, we obtained the RNA-seq data of 1086 patients from The Cancer Genome Atlas (TCGA) database. We calculated the proportions of tumor-infiltrating immune cells (TICs) and immune and stromal components using the CIBERSORT and ESTIMATE methods, and we screened differentially expressed genes (DEGs). …”
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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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Prognostic value of FCER1G expression and M2 macrophage infiltration in esophageal squamous cell carcinoma by Wei Peng, Yali Zhao, Ningning Yang, Yan Fang, Yintong Wu, Zhenzhong Feng, Qiang Wu, Xian Wang

“…Methods The expression of FCER1G and its prognostic value in ESCC was examined by The Cancer Genome Atlas and Gene Expression Omnibus databases. We also evaluated the relationship between FCER1G expression and 22 TIICs. …”
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Combining extracellular matrix proteome and phosphoproteome of chickpea and meta‐analysis reveal novel proteoforms and evolutionary significance of clade‐specific wall‐associated e... by Kanika Narula, Arunima Sinha, Pooja Choudhary, Sudip Ghosh, Eman Elagamey, Archana Sharma, Atreyee Sengupta, Niranjan Chakraborty, Subhra Chakraborty

“…We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta‐analyses of 74 plant matrisomes. …”
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Integrating multiomics analysis and machine learning to refine the molecular subtyping and prognostic analysis of stomach adenocarcinoma by Miaodong Wang, Qin He, Zeshan Chen, Yijue Qin

“…We downloaded the multiomics data of STAD patients in The Cancer Genome Atlas (TCGA)-STAD cohort, which included mRNA, microRNA, long non-coding RNA, somatic mutation, and DNA methylation data, from the sxdyc website. …”
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Критичний аналіз гелієвих газобалонних систем наддування паливних баків ракетних двигунів by Юрій Мітіков, Максим Седченко

“…Достатньо навести як приклад РРД РН «Зеніт», «Циклон-4М, «Маяк» (Україна), Antares (США та Україна), Atlas-V, Falcon 9 (США), "Чанчжен-7" та "Чанчжен-9 (КНР), КSLV-I, КSLV-II (Південна Корея) та ін. …”
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In-depth characterization of miRNome in papillary thyroid cancer with BRAF V600E mutation by Azliana Mohamad Yusof, Francis Yew Fu Tieng, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Isa Mohamed Rose, Sazuita Saidin, Rahman Jamal, Imilia Ismail, Nurul-Syakima Ab Mutalib

“…MiRNAs differentially expressed between BRAF V600E-positive and BRAF V600E-negative PTC tissues were validated in silico using The Cancer Genome Atlas (TCGA) THCA datasets containing 420 samples. …”
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Fatty acid metabolism-related signature suggests an oncogenic role of TEKT1 in endometrial cancer by Zhikai Xiahou, Hong Xiao, Yafeng Song, Xin Xu

“…Materials and methods: A total of 309 fatty acid metabolism relative genes were analyzed in the endometrial cancer cohort from The Cancer Genome Atlas. Dataset GSE216872 was applied for external validation. …”
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The Identification and Validation of a Robust Immune-Associated Gene Signature in Cutaneous Melanoma by Le-Bin Song, Jiao-Chen Luan, Qi-Jie Zhang, Lin Chen, Hao-Yang Wang, Xue-Chen Cao, Ning-Hong Song, Yan Lu

“…Methods. 434 melanoma patients were extracted from The Cancer Genome Atlas (TCGA) database, and 1811 IAGs were downloaded from the ImmPort database in our retrospective study. …”
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Identification of Ferroptosis-Associated Long Noncoding RNA Prognostic Model and Tumor Immune Microenvironment in Thyroid Cancer by Yongjian Lin, Fu Gan, Xiaoyu He, Huachu Deng, Yong Li

“…The TC lncRNA data were extracted from RNA sequencing files of The Cancer Genome Atlas (TCGA). Then, we performed a two-cluster analysis and grouped 502 patients with TC in a 7 : 3 ratio. …”
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Macrophages Phenotype Regulated by IL-6 Are Associated with the Prognosis of Platinum-Resistant Serous Ovarian Cancer: Integrated Analysis of Clinical Trial and Omics by Xiaoqing Wu, Wenping Lu, Chaojie Xu, Cuihong Jiang, Zhili Zhuo, Ruipeng Wang, Dongni Zhang, Yongjia Cui, Lei Chang, Xi Zuo, Ya’nan Wang, Heting Mei, Weixuan Zhang, Mengfan Zhang, Chen Li

“…We used ESTIMATE to calculate the number of immune and stromal components in high-grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas database. The differential expression genes (DEGs) were analyzed via protein–protein interaction network, Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis to reveal major pathways of DEGs. …”
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Transcriptomic analysis of Medicago truncatula calli with MtWOX9-1 overexpression by V. E. Tvorogova, E. Y. Krasnoperova, A. A. Kudriashov, K. A. Kuznetsova, E. A. Potsenkovskaya, Y. A. Fedorova, L. A. Lutova

“…Using Medicago Truncatula Gene Expression Atlas, we also identified a group of genes  coding for transcription factors that were both coexpressed with MtWOX9-1 in different plant organs  and differentially expressed in our samples. …”
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Relationship between inherited genetic variation and survival from colorectal cancer stratified by tumour location by Christopher Wills, Katie Watts, Amy Houseman, Timothy S. Maughan, David Fisher, Nada A. Al-Tassan, Richard S. Houlston, Valentina Escott-Price, Jeremy P. Cheadle

“…We investigated the relationship between Phosphatidylinositol 4-Kinase Type 2 Beta (PI4K2B) expression in colorectal tumours and survival in 597 patients from The Human Protein Atlas (THPA). We also analysed 3 SNPs previously associated with survival by anatomical site. …”
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Prognostic Significance and Therapeutic Potential of SERPINE1 in Head and Neck Squamous Cell Carcinoma by Changyu Zhu, Heshu Liu, Zhixin Li, Yijun Shi, Jingyang Zhao, Yuping Bai, Qian Chen, Wei Li

“…Methods and Results In this study, we delved into the variations in gene mutation, methylation patterns, and expression levels of SERPINE1 in head and neck squamous cell carcinoma (HNSCC) and normal tissues, leveraging comprehensive analyses of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. …”
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The experience of living with human immunodeficiency virus among adolescents at Felege Hiwot Comprehensive Specialized Hospital Bahir-Dar, Northwest Ethiopia, A phenomenological st... by Bazezew Asfaw Guadie, Minyichil Birhanu Belete, Meseret Mekuriaw Beyene, Ayalew Kassie Melese, Tarik Yenew Tessema, Yinager Workineh

“…For additional analysis, the translated data was entered into the Atlas.ti.8 program. To demonstrate findings, the inductive thematic analysis technique was applied using illustrative quotes. …”
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Annotation-free deep learning algorithm trained on hematoxylin & eosin images predicts epithelial-to-mesenchymal transition phenotype and endocrine response in estrogen receptor-po... by Kaimin Hu, Yinan Wu, Yajing Huang, Meiqi Zhou, Yanyan Wang, Xingru Huang

“…To confirm the presence of morphological discrepancies in tumor tissues of ER+ breast cancer classified as epithelial- and mesenchymal-phenotypes according to EMT-related transcriptional features, we trained deep learning algorithms based on EfficientNetV2 architecture to assign the phenotypic status for each patient utilizing hematoxylin & eosin (H&E)-stained slides from The Cancer Genome Atlas database. Our classifier model accurately identified the precise phenotypic status, achieving an area under the curve (AUC) of 0.886 at the tile-level and an AUC of 0.910 at the slide-level. …”
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Diagnosis of invasive encapsulated follicular variant papillary thyroid carcinoma by protein-based machine learning by Truong Phan-Xuan Nguyen, Minh-Khang Le, Sittiruk Roytrakul, Shanop Shuangshoti, Nakarin Kitkumthorn, Somboon Keelawat

“…Additionally, we analyzed the performance of single-protein/gene receiver operating characteristic in differentiating the invasive encapsulated follicular variant of papillary thyroid carcinoma from others within The Cancer Genome Atlas projects, which yielded an AUC >0.5. Conclusions We demonstrated that integration of high-throughput proteomics with machine learning can effectively differentiate the invasive encapsulated follicular variant of papillary thyroid carcinoma from other follicular pattern thyroid tumors.…”
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Comprehensive analysis of heat shock protein 110, 90, 70, 60 families and tumor immune microenvironment characterization in clear cell renal cell carcinoma by Wenjing Liao, Mao Huang, Xiaoyi Du, Liangdan Tang, Junwu Li, Qin Tang

“…The data obtained from the Cancer Genome Atlas (TCGA) were applied to determine the differential expression of HSPs in normal tissues and ccRCC. …”
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