Integrating single-cell RNA-seq and bulk RNA-seq to explore prognostic value and immune landscapes of methionine metabolism-related signature in breast cancer by Yanxian Gao, Ziyu Feng, Hailong Zhao, Xinghai Liu, Muyu Zhu, Xiafei Yu, Xiaoan Liu, Xian Wu, Jing Tao

“…Breast cancer cell lines have been identified as methionine-dependent, and methionine restriction has been proposed as a potential cancer treatment strategy.MethodsWe integrated transcriptomic and single-cell RNA sequencing (ScRNA-seq) analyses based on The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. …”
Get full text

Differential impact of TIM-3 ligands on NK cell function by Xin Zhang, Lazar Vujanovic, Riyue Bao, Robert L Ferris, Tullia C Bruno, Aditi Kulkarni, Hridesh Banerjee, Housaiyin Li, Juncheng Wang, Lawrence P Kane, Pragati Upadhyay, Jennifer L Anderson, Onyedikachi Victor Onyekachi, Lidia M R B Arantes

“…Finally, The Cancer Genome Atlas survival analysis and digital spatial profiling were employed to study the potential impact of etiology-associated differences on patients with HNSCC outcomes.Results We demonstrate that TIM-3 is highly prevalent on circulating and tumor-infiltrating NK cells. …”
Get full text

Prognostic significance of p27 in colorectal cancer: a meta-analysis and bioinformatics analysis by Jing Zou, Dong Wang, Gaoping Yin, Kexiang Lu, Kaibin Chang, He Li

“…In addition, we used Gene Expression Profiling Interactive Analysis (GEPIA), University of Alabama at Birmingham’s Cancer Data Analysis Portal (UALCAN), and the Human Protein Atlas (HPA) to validate our results.ResultsThrough an extensive examination of four prominent databases, a total of 21 original articles encompassing a cohort of 3,378 patients were identified. …”
Get full text

THE ROLE OF N. I. VAVILOV AND VIR’S SCIENTISTS IN DESERT RECLAMATION by N. I. Dzyubenko, A. A. Kochegina

“…Employees of the Department of Perennial Forage Crop Genetic Resources of VIR took part in the mapping of arid areas and sustainable fodder plant distribution for the Internet publication “Interactive Agricultural Ecological Atlas of Russia and Neighboring Countries Economic Plants and their Diseases, Pests and Weeds.” …”
Get full text

Upregulated SAE1 Drives Tumorigenesis and Is Associated with Poor Clinical Outcomes in Breast Cancer by Hong Liu, Jing Wang, Yunhai Li, Feng Luo, Lei Xing

“…Bioinformatics analysis was applied to analyze SAE1 expression in BC and normal breast tissues, its relationship with clinicopathologic characteristics and prognosis in BC patients, and data from the Cancer Genome Atlas database and Gene Expression Omnibus dataset. …”
Get full text

Spatial transcriptomics reveals unique metabolic profile and key oncogenic regulators of cervical squamous cell carcinoma by Limin Zhou, Jiejie Liu, Peipei Yao, Xing Liu, Fei Chen, Yu Chen, Li Zhou, Chao Shen, You Zhou, Xin Du, Junbo Hu

“…We also employed The Cancer Genome Atlas (TCGA) database to examine the analysis results of ST data. …”
Get full text

The lysosome-related characteristics affects the prognosis and tumor microenvironment of lung adenocarcinoma by Wuguang Chang, Wuyou Gao, Yawei Wu, Bin Luo, Lekai Zhong, Leqi Zhong, Wenqian Lin, Zhesheng Wen, Youfang Chen

“…However, there are few studies on lysosome-associated genes (LAGs) in lung adenocarcinoma (LUAD).MethodsBulk RNA-seq of LUAD was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The lysosome risk signature was constructed after univariate and least absolute shrinkage and selection operator (Lasso) cox regression analysis of the TCGA training set, and its capability was validated by additional validation sets from GEO. …”
Get full text

RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia by Tim Kong, Angelo B. A. Laranjeira, Christopher T. Letson, LaYow Yu, Shuyang Lin, Jared S. Fowles, Daniel A. C. Fisher, Sherwin Ng, Wei Yang, Fan He, Minyoung Youn, Kailen Mark, Ana San Jose, Jingxian Liu, Alexander B. Kim, Maggie J. Cox, Mary C. Fulbright, Aarthi Jayanthan, Gerrit Los, Stacey L. Rentschler, Li Ding, Kathleen M. Sakamoto, Sandra E. Dunn, Grant A. Challen, Stephen T. Oh

“…Here, we establish a comprehensive transcriptional atlas across the spectrum of myeloproliferative neoplasms (MPN) and secondary acute myeloid leukemia (sAML) through RNA-sequencing of 158 primary samples encompassing CD34+ hematopoietic stem/progenitor cells and CD14+ monocytes. …”
Get full text

Glioma Image-Level and Slide-Level Gene Predictor (GLISP) for Molecular Diagnosis and Predicting Genetic Events of Adult Diffuse Glioma by Minh-Khang Le, Masataka Kawai, Kenta Masui, Takashi Komori, Takakazu Kawamata, Yoshihiro Muragaki, Tomohiro Inoue, Ippei Tahara, Kazunari Kasai, Tetsuo Kondo

“…In this study, the Cancer Genome Atlas whole-slide images (WSIs) were used to train the model. …”
Get full text

A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer by Veronica Rendo, Michael Schubert, Nicholas Khuu, Maria F. Suarez Peredo Rodriguez, Declan Whyte, Xiao Ling, Anouk van den Brink, Kaimeng Huang, Michelle Swift, Yizhou He, Johanna Zerbib, Ross Smith, Jonne Raaijmakers, Pratiti Bandopadhayay, Lillian M. Guenther, Justin H. Hwang, Amanda Iniguez, Susan Moody, Ji-Heui Seo, Elizabeth H. Stover, Levi Garraway, William C. Hahn, Kimberly Stegmaier, René H. Medema, Dipanjan Chowdhury, Maria Colomé-Tatché, Uri Ben-David, Rameen Beroukhim, Floris Foijer

“…We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. …”
Get full text

CYFIP2: potential pancreatic cancer biomarker and immunotherapeutic target by Cong Xiao, Xiaojuan Zhang, Bobo Hou, Ping Wan, Zhenjun Cao, Xuefeng Rao

“…Methods The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) database, CELL and GEO databases were utilized to explore the distribution of the CYFIP2 gene in human cancers. …”
Get full text

Autophagy activation in response to cigarette smoke: Exploring the disparity in laryngeal cancer incidence and outcomes between sexes in South Korea by Min Ji Kim, Jisu Hong, Hyo Won Chang, Yun-Hee Lee, Jun-Pyo Myong, Ah Ra Jung, Yoon Se Lee, Minsu Kwon

“…In addition, to explore the relationship between the level of autophagy-related gene expression and clinical features, female LC patients were compared with male patients through an analysis of data from The Cancer Genome Atlas (TCGA). Results: In the NHIS data analyses, male LC patients had an 11 times higher incidence than female patients, even after adjusting for smoking and age. …”
Get full text

Presenting a model to explain unfavorable risk and favorable risk according to psychological variables in predicting market fluctuations in the Iranian capital market. by Hasan Rezaeikangi, Mahdi Mohammad Bagheri, Hojat Babaei, Ali Raeispour Rajabali

“…The method of data collection is referring to documents and semi-structured interviews. For data analysis, Atlas ti software was used to code the interviews. …”
Get full text

Immune Cell-Based versus Albumin-Based Ratios as Outcome Predictors in Critically Ill COVID-19 Patients by Zeba S, Surbatovic M, Udovicic I, Stanojevic I, Vojvodic D, Rondovic G, Mladenovic K, Abazovic T, Hasanovic A, Ilic AN, Abazovic D, Khan W, Djordjevic D

“…Snjezana Zeba,1 Maja Surbatovic,2 Ivo Udovicic,1 Ivan Stanojevic,3 Danilo Vojvodic,3 Goran Rondovic,1 Katarina Mladenovic,1 Tanja Abazovic,2 Almina Hasanovic,4 Aleksandra N Ilic,5 Dzihan Abazovic,6 Wasim Khan,7 Dragan Djordjevic1 1Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Faculty of Medicine of the Military Medical Academy, University of Defense, Belgrade, Serbia; 2Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Belgrade, Serbia; 3Institute for Medical Research, Military Medical Academy, Faculty of Medicine of the Military Medical Academy, University of Defense, Belgrade, Serbia; 4Nephrology Clinic, Military Medical Academy, Belgrade, Serbia; 5Faculty of Medicine, University of Pristina, Kosovska Mitrovica, Serbia; 6Atlas Hospital, Belgrade, Serbia, Aba Medica Healthcare Centre, Ulcinj, Montenegro; 7Division of Trauma & Orthopaedic Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UKCorrespondence: Maja Surbatovic, Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, 17 Crnotravska Street, Belgrade, 11000, Serbia, Tel +381 11 2665 125, Email maja.surbatovic@gmail.comPurpose: The aim of the retrospective, single-center study was to assess the prognostic value of immune cell-based and albumin-based ratios regarding lethal outcome in critically ill COVID-19 patients.Patients and Methods: We analyzed 612 adult critically ill COVID-19 patients admitted to the intensive care unit (ICU) between April 2020 and November 2022. …”
Get full text

Identification of EARS2 as a Potential Biomarker with Diagnostic, Prognostic, and Therapeutic Implications in Colorectal Cancer by Wang L, Deng X, Tang J, Gong Y, Bu S, Li Z, Liao B, Ding Y, Dai T, Liao Y, Li Y

“…This study identifies key genes associated with lactic acid metabolism and explore their impact on CRC.Patients and Methods: This study utilized data from The Cancer Genome Atlas, Gene Expression Omnibus, other public databases, and our institutional resources. …”
Get full text

Dysfunctional large-scale brain networks in drug-naïve depersonalization-derealization disorder patients by Sisi Zheng, Mingkang Song, Nan Song, Hong Zhu, Xue Li, Dongqing Yin, Shanshan Liu, Yan Zhao, Meng Fang, Yanzhe Ning, Hongxiao Jia

“…After constructing large-scale brain networks, we calculated within‐and between‐network functional connectivity (FC) using the Schaefer and Tian atlas. The Support Vector Machine (SVM) model was employed to classify DPRD patients and provide features for DPRD patients concerning the dysfunctional large-scale brain networks. …”
Get full text

Comprehensive Analysis of m5C RNA Methylation Regulator Genes in Clear Cell Renal Cell Carcinoma by Jiajin Wu, Chao Hou, Yuhao Wang, Zhongyuan Wang, Pu Li, Zengjun Wang

“…Based on The Cancer Genome Atlas (TCGA) database, the expression patterns of twelve m5C regulators and matched clinicopathological characteristics were downloaded and analyzed. …”
Get full text

The Multifaceted Roles of Myrrha in the Treatment of Breast Cancer: Potential Therapeutic Targets and Promises by Anwar Shams MD, MSc, PhD, Abdullah Ahmed Alzahrani, Taghreed A Ayash MSc, PhD, Shadi Tamur MD, FRCPC, FAAP, Majed AL-Mourgi MD, FRCS, FCCP, FACS

“…Method: The identified targets’ expression profiles were determined at the mRNA and protein levels using The Breast Cancer Gene-Expression Miner v5.0 (bcGen-ExMiner v5.0) and The Human Protein Atlas datasets, respectively. A gene signature composed of the specifically designated genes was constructed, and its association with different breast cancer molecular subtypes was investigated through the Gene expression-based Outcome for Breast Cancer (GOBO) online tool. …”
Get full text

miR-9-5p/HMMR regulates the tumorigenesis and progression of clear cell renal cell carcinoma through EMT and JAK1/STAT1 signaling pathway by Xinyang Niu, Dingheng Lu, Weitao Zhan, Jiazhu Sun, Yuxiao Li, Yuchen Shi, Kai Yu, Suyuelin Huang, Xueyou Ma, Xiaoyan Liu, Ben Liu

“…Methods We used The Cancer Genome Atlas (TCGA) database to preliminarily investigate HMMR expression and function in ccRCC and the data for 19 samples from the NCBI GEO database (GSE207493) for single-cell analysis. …”
Get full text

CT45A1‐mediated MLC2 (MYL9) phosphorylation promotes natural killer cell resistance and outer cell fate in a cell‐in‐cell structure, potentiating the progression of microsatellite... by Hao‐Wei Teng, Hsiang‐Yueh Huang, Chun‐Chi Lin, Yuh‐Ching Twu, Wen‐Hao Yang, Wen‐Chun Lin, Hsin‐Yi Lan, Yen‐Yu Lin, Wei‐Lun Hwang

“…We aimed to identify the tumor‐autonomous regulators determining these heterogeneous clinical outcomes. The Cancer Genome Atlas (TCGA) dataset was used to identify regulators in MSI‐H CRC patients with unfavorable outcomes. …”
Get full text