UBE2J1 is identified as a novel plasma cell-related gene involved in the prognosis of high-grade serous ovarian cancer by Yunjie Tian, Ruoyu Dong, Yingxia Guan, Ying Wang, Wei Zhao, Jun Zhang, Shan Kang

“…Methods We utilized single-cell sequencing data from the Gene Expression Omnibus (GEO) database to identify key immune cell types within HGSOC tissues and to extract related markers via the Seurat package. …”
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RAS, a Pentatricopeptide Repeat Protein, Interacts with OsTRX z to Regulate Chloroplast Gene Transcription and RNA Processing by Zhennan Qiu, Shiyong Wen, Peinan Sun, Dongdong Chen, Chunmiao Wang, Xiliang Song, Liying Xiao, Peiliang Zhang, Dongying Zhao, Cuiping Wen, Peiyan Guan, Xuechu Du, Yinghui Sun, Chenshan Xu, Jian Song

“…Collectively, our findings highlight the critical role of RAS in chloroplast development, as it is involved in RNA processing and the regulation of chloroplast gene expression.…”
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Combined metabolomic and transcriptomic analysis to reveal the response of rice to Mn toxicity stress by Feng Li, Yushuang Yao, Jiapeng Ma, Zhengwei Wu, Dianfeng Zheng, Yingbin Xue, Ying Liu

“…Excessive manganese (Mn) concentrations affect plant gene expression, alter metabolite content, and impede plant growth. …”
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Identification and verification of autophagy-related gene signatures and their association with immune infiltration and drug responsiveness in epilepsy by Han-han He, Xiao-ge Zhang, Fen-fang Chen

“…However, the precise mechanisms by which autophagy deficiencies involved in epileptogenesis are still not fully understood.MethodsTwo datasets of epilepsy (GSE143272 and GSE256068) were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were employed to screen for autophagy related differential expression genes (ARDEGs) in GSE143272 database. …”
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Dietary addition of compound organic acids improves the growth performance, carcass trait, and body health of broilers by Fang Cai, Meiping Huang, Wei Liu, Xiaoling Wan, Kai Qiu, Xiao Xu

“…Overall, the acidifier effectively improved broiler growth performance during the early development phase primarily by enhancing hepatic lipid metabolism, antioxidant capacity, and immune function.ConclusionThese results suggest that the acidifier may accelerate liver lipid metabolism in broilers by modulating the gene expression profiles involved in lipid metabolism.…”
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Circ_0001084/miR-181c-5p/PTPN4 Axis Mitigates Cardiomyocyte Injury by Modulating the TLR4/NF-κB Pathway: Insights into Therapeutic Potential for Myocardial Reperfusion Injury by Deng H, Fan Q, Huang L, Ouyang W, Zhu W

“…Non-coding RNAs, including miRNAs, have been increasingly recognized for their roles in regulating cardiomyocyte responses to hypoxia/reoxygenation (H/R) injury. miR-181c-5p, in particular, has been implicated in inflammatory and apoptotic processes, suggesting its potential involvement in exacerbating cellular damage.Methods: This study combined bioinformatic and experimental techniques to investigate myocardial injury. Gene expression data from the GEO database were analyzed, and HL-1 cardiomyocytes were used in a hypoxia/reoxygenation model to mimic reperfusion injury. …”
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Application of deep learning models on single-cell RNA sequencing analysis uncovers novel markers of double negative T cells by Tian Xu, Qin Xu, Ran Lu, David N. Oakland, Song Li, Liwu Li, Christopher M. Reilly, Xin M. Luo

“…However, advanced deep learning models such as Single Cell Variational Inference (scVI) have the capability to capture nonlinear gene expression patterns in the sequencing data. In this study, employing the deep learning methodology, we have revealed novel markers for splenic DNT cells in C57BL/6 mice which were validated with flow cytometry analysis. …”
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Comparative Analysis of <i>In Vivo</i> and <i>In Vitro</i> Virulence Among Foodborne and Clinical <i>Listeria monocytogenes</i> Strains by Hui Yan, Biyao Xu, Binru Gao, Yunyan Xu, Xuejuan Xia, Yue Ma, Xiaojie Qin, Qingli Dong, Takashi Hirata, Zhuosi Li

“…In addition, ST121 exhibited significantly higher <i>hly</i>, <i>inlA</i>, <i>inlB</i>, <i>prfA</i>, <i>plcA</i>, and <i>plcB</i> gene expression compared with other STs. A gray relation analysis showed a high correlation between the toxicity of <i>G. mellonella</i> and the expression of the <i>hly</i> and <i>inlB</i> genes; in addition, <i>L. monocytogenes</i> may have a consistent virulence mechanism involving hemolysis activity and cytotoxicity. …”
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Identification of quality markers and mechanisms of Anzi Tiaochong Fang in the treatment of antiphospholipid syndrome-related recurrent pregnancy loss: chemical analysis, network p... by Shan He, Fei Ma, Jia Li, Da-yan Liu, Zhi-wei Wang, Peng-dian Chen, Jia-man Wu, Hong Chang, Yan Ning

“…APS-RPL targets were identified using databases such as HERB, similarity ensemble approach, PharmMapper, Swiss Target Prediction, Gene Expression Omnibus, Genecards, and DisGeNET. GO and Reactome analyses were conducted using KOBAS-i. …”
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A Genome-Wide Analysis of Long Noncoding RNAs in Circulating Leukocytes and Their Differential Expression in Type 1 Diabetes Patients by Yihan Liu, Xiaoming Du, Jia Cui, Changlong Li, Meng Guo, Jianyi Lv, Xin Liu, Jingtao Dou, Xiaoyan Du, Hongjuan Fang, Zhenwen Chen

“…Long noncoding RNAs (lncRNAs) regulate gene expression at different levels in various diseases, including type 1 diabetes (T1D). …”
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Single-cell sequencing elucidates the mechanism of NUSAP1 in glioma and its diagnostic and prognostic significance by Meng-Yu Zhao, Zhao-Lei Shen, Hongzhen Dai, Wan-Yan Xu, Li-Na Wang, Yu- Gu, Jie-Hui Zhao, Tian-Hang Yu, Cun-Zhi Wang, Jia-feng Xu, Guan-Jun Chen, Dong-Hui Chen, Wen-Ming Hong, Wen-Ming Hong, Fang Zhang

“…By integrating single-cell sequencing analysis with foundational experiments, we investigated the molecular variations and cellular interactions within neural glioma cell subpopulations during tumor progression.ResultsOur single-cell sequencing analysis revealed distinct gene expression patterns across glioma cell subpopulations. …”
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Posttraumatic Cranial Cystic Fibrous Dysplasia by Arata Tomiyama, Kazuya Aoki, Haruo Nakayama, Hideaki Izukura, Hitoshi Kimura, Jun-ichi Harashina, Keisuke Ito, Morito Hayashi, Norihiko Saito, Takatoshi Sakurai, Toshiaki Oharaseki, Hitoshi Terada, Satoshi Iwabuchi

“…Previous studies have suggested that c-fos gene expression is a key mechanism in injury-induced FD.…”
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Exploring the comorbidity mechanisms between atherosclerosis and hashimoto’s thyroiditis based on microarray and single-cell sequencing analysis by Yirong Ma, Shuguang Wu, Junyu Lai, Qiang Wan, Jingxuan Hu, Yanhong Liu, Ziyi Zhou, Jianguang Wu

“…We obtained relevant datasets for AS and HT from the Gene Expression Omnibus (GEO). By employing the Limma package, we pinpointed common differentially expressed genes (DEGs) and discerned co-expression modules linked to AS and HT via Weighted Gene Co-expression Network Analysis (WGCNA). …”
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Screening of necroptosis-related genes and evaluating the prognostic capacity, clinical value, and the effect of their copy number variations in acute myeloid leukemia by Dake Wen, Ru Yan, Lin Zhang, Haoyang Zhang, Xuyang Chen, Jian Zhou

“…Methods Necroptosis-related differentially expressed genes (NRDEGs) were identified after intersecting differentially expressed genes (DEGs) from the Gene Expression Omnibus(GEO) database with NRGs from GeneCards, the Molecular Signatures Database (MSigDB) and literatures. …”
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Dual role of Cathepsin S in cutaneous melanoma: insights from mendelian randomization and bioinformatics analysis by Linsa Zhou, Qiang Zhou, Qian Guo, Peng Lai, Chen Rui, Wanqing Li, Xuemei Chen, Yue Zhuo, Xiaoping Zhong, Sen Lin

“…Here, we investigated the causal relationship between CM and genes related to sun-damaged skin, exploring specific target genes through various bioinformatics analyses. Methods The Gene Expression Omnibus (GEO) database was used to obtain differential genes for CM and normal skin, and the Genome-Wide Association Studies (GWAS) analysis offered summary-level melanoma data for CM. …”
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Ochratoxin A induces immunotoxicity by targeting Annexin A1 mediated neutrophil apoptosis in zebrafish by Yihong Zheng, Yinuo Liu, Jin Tian, Shuhong Liu, Gaowei Ma, Yupeng Xie, Chenhua Zheng, Zekai Wu

“…Transcriptome sequencing analysis was performed to identify changes in gene expression. Additionally, the potential therapeutic effect of aesculetin was evaluated.ResultsOur results demonstrated that exposure to OTA inhibited embryonic development and induced malformations in a concentration-dependent manner. …”
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Intraindividual variation in histone acetylation and its impact on autoimmune thyroid diseases by Emi Haga, Naoya Inoue, Yoshinori Iwatani, Yuya Arakawa, Emi Morita, Hidemi Hashimoto, Yusuke Noguchi, Yoh Hidaka, Mikio Watanabe

“…Histone acetylation, especially that of histone H3, is an epigenetic mechanism that regulates gene expression and is associated with the development of autoimmune diseases. …”
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Antioxidant and Anti-Inflammatory Potential of Cymbopogon nardus Ethanol Extract on 3T3-L1 Cells by Rohmawaty E, Wiraswati HL, Zahra TA, Amalina SN, Ramadhanti J, Rosdianto AM, Laelalugina A, Nasution GTD, Kamisah Y

“…Additionally, the effects of the extract on the gene expression of hypoxia-inducible factor 1α (HIF-1α) in menadione-induced 3T3-L1 cells, as well as interleukin-6 (IL-6) and cyclooxygenase-2 (COX-2) in lipopolysaccharide (LPS)-induced 3T3-L1 cells, were investigated.Results: Phytochemical screening revealed the presence of phenolics, tannins, alkaloids, and flavonoids in the ethanolic extracts. …”
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Dysfunction in mitochondrial electron transport chain drives the pathogenesis of pulmonary arterial hypertension: insights from a multi-omics investigation by Xin Zhang, Jieling Li, Minyi Fu, Xijie Geng, Junjie Hu, Ke-Jing Tang, Pan Chen, Jianyong Zou, Xiaoman Liu, Bo Zeng

“…Methods We integrated three microarray datasets from the Gene Expression Omnibus (GEO), including 222 lung samples (164 PAH, 58 controls), for differential expression and functional enrichment analyses. …”
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Role of Cathepsin S in Periodontal Inflammation and Infection by S. Memmert, A. Damanaki, A. V. B. Nogueira, S. Eick, M. Nokhbehsaim, A. K. Papadopoulou, A. Till, B. Rath, S. Jepsen, W. Götz, C. Piperi, E. K. Basdra, J. A. Cirelli, A. Jäger, J. Deschner

“…In vivo, gingival tissue biopsies from rats with ligature-induced periodontitis and from periodontitis patients were also analyzed at transcriptional and protein levels. Multiple gene expression changes due to interleukin-1β and F. nucleatum were observed in vitro. …”
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