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JOURNAL ARTICLE
Zhihua Chen, Wei Hu, Jiahong Wang, Donggen Rao, Jianming Zhu
The diagnostic biomarkers associated with ischemic stroke (IS) that may have clinical utility remain elucidated. Thus, the potential functional lncRNAs in IS were explored. The Gene Expression Omnibus database provided the transcriptome profile of IS for download. WGCNA analysis and integrated bioinformatics were used to find genes that were differentially expressed (DEGs). The Starbase database created the lncRNA-based ceRNA network. In order to investigate the molecular mechanism and involved pathways of DEGs in IS, functional enrichment analysis was carried out...
March 31, 2024: Cellular and Molecular Biology
#22
JOURNAL ARTICLE
Shi-Wei Long, Shi-Hong Li, Jian Li, Yang He, Bo Tan, Hao-Han Jing, Wei Zheng, Juan Wu
RESEARCH BACKGROUND AND PURPOSE: Osteoporosis (OP) is one of the most common bone diseases worldwide, characterized by low bone mineral density and susceptibility to pathological fractures, especially in postmenopausal women and elderly men. Ferroptosis is one of the newly discovered forms of cell death regulated by genes in recent years. Many studies have shown that ferroptosis is closely related to many diseases. However, there are few studies on ferroptosis in osteoporosis, and the mechanism of ferroptosis in osteoporosis is still unclear...
April 22, 2024: BMC Medical Genomics
#23
JOURNAL ARTICLE
Hua Ji, Zheng Tang, Kexin Jiang, Shuang Lyu, Yiwen Zhao, Jiajie Feng, Ruiwu Dai, Hongyin Liang
BACKGROUND: Acute pancreatitis (AP) has become a significant global health concern, and a high body mass index (BMI) has been identified as a key risk factor exacerbating this condition. Within this context, lipid metabolism assumes a critical role. The complex relationship between elevated BMI and AP, mediated by lipid metabolism, markedly increases the risk of complications and mortality. This study aimed to accurately define the correlation between BMI and AP, incorporating a comprehensive analysis of the interactions between individuals with high BMI and AP...
April 22, 2024: Lipids in Health and Disease
#24
JOURNAL ARTICLE
Rui Shi, Chunyun Bai, Shibo Sun, Fang Wang, Chaozhong Li, Chongyu Wang, Lidan Hu, Ziwen Zhao, Qiuzhe Guo, Guanhua Du, Dan Xu, Alex F Chen, Weimin Yang
OBJECTIVES: Sepsis is a life-threatening infectious disease in which an immune inflammatory response is triggered. The potential effect of ferroptosis-related genes (FRGs) in inflammation of sepsis remained unclear. We focused on identifying and validating core FRGs and their association with immune infiltration in blood from currently all patients with sepsis. METHODS: All current raw data of septic blood were obtained from Gene Expression Omnibus. After removing the batch effect merging into a complete dataset and obtaining Diferentially expressed genes (DEGs)...
April 20, 2024: Gene
#25
JOURNAL ARTICLE
Tianlong Ling, Cheng Zhang, Ye Liu, Chunhui Jiang, Lei Gu
Liver metastasis (LM) is an important factor leading to colorectal cancer (CRC) mortality. However, the effect of T-cell exhaustion on LM in CRC is unclear. Single-cell sequencing data derived from the Gene Expression Omnibus database. Data were normalized using the Seurat package and subsequently clustered and annotated into different cell clusters. The differentiation trajectories of epithelial cells and T cells were characterized based on pseudo-time analysis. Single-sample gene set enrichment analysis (ssGSEA) was used to calculate enrichment scores for different cell clusters and to identify enriched biological pathways...
April 2024: Journal of Cellular and Molecular Medicine
#26
JOURNAL ARTICLE
Ruihao Zhang, Guangsheng Zhu, Zaishan Li, Zhenzhen Meng, Hua Huang, Chen Ding, Yanan Wang, Chen Chen, Yongwen Li, Hongyu Liu, Jun Chen
BACKGROUND: Integrin subunit alpha L (ITGAL) encodes an integrin component of LFA-1 and is a membrane receptor molecule widely expressed on leukocytes. It plays a key role in the interaction between white blood cells and other cells. There was a significant correlation between the expression of ITGAL and the tumor microenvironment in a number of cancers. However, experimental studies targeting ITGAL and immune cell infiltration in non-small-cell lung cancer (NSCLC) and the response to immune checkpoint inhibitor therapy are lacking...
2024: Frontiers in Immunology
#27
JOURNAL ARTICLE
Mingjie Shi, Yue Wei, Runmin Guo, Fei Luo
BACKGROUND: Sepsis is a major contributor to morbidity and mortality among hospitalized patients. This study aims to identify markers associated with the severity and prognosis of sepsis, providing new approaches for its management and treatment. METHODS: Data were mined from the Gene Expression Omnibus (GEO) databases and were analyzed by multiple statistical methods like the Spearman correlation coefficient, Kaplan-Meier analysis, Cox regression analysis, and functional enrichment analysis...
2024: Journal of Inflammation Research
#28
JOURNAL ARTICLE
Xuewei Liu, Huangchao Jia, Liyun Wang, Ziwen Wang, Mengyue Xu, Yunfei Li, Ronghui Wang
OBJECTIVE: To screen for the key characteristic genes of the psoriasis vulgaris (PV) patients with different Traditional Chinese Medicine (TCM) syndromes, including blood-heat syndrome (BHS), blood stasis syndrome (BSS), and blood-dryness syndrome (BDS), through bioinformatics and machine learning and to provide a scientific basis for the clinical diagnosis and treatment of PV of different TCM syndrome types. METHODS: The GSE192867 dataset was downloaded from Gene Expression Omnibus (GEO)...
March 20, 2024: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
#29
JOURNAL ARTICLE
Qiao Zhou, Jian Liu, Yan Zhu, Yuan Wang, Guizhen Wang, Yajun Qi, Yuedi Hu
OBJECTIVE: To identify inflamm-aging related biomarkers in osteoarthritis (OA). METHODS: Microarray gene profiles of young and aging OA patients were obtained from the Gene Expression Omnibus (GEO) database and aging-related genes (ARGs) were obtained from the Human Aging Genome Resource (HAGR) database. The differentially expressed genes of young OA and older OA patients were screened and then intersected with ARGs to obtain the aging-related genes of OA. Enrichment analysis was performed to reveal the potential mechanisms of aging-related markers in OA...
March 20, 2024: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
#30
JOURNAL ARTICLE
Dongfeng Jiang, Xiaoyi Song, Liyu Yang, Li Zheng, Kaifeng Niu, Hui Niu
Bovine tuberculosis (bTB) is a chronic zoonotic disease caused by Mycobacterium bovis . A large number of cattle are infected with bTB every year, resulting in huge economic losses. How to control bTB is an important issue in the current global livestock economy. In this study, the original transcriptome sequences related to this study were obtained from the dataset GSE192537 by searching the Gene Expression Omnibus (GEO) database. Our differential gene analysis showed that there were obvious biological activities related to immune activation and immune regulation in the early stage of bTB...
2024: Frontiers in Veterinary Science
#31
Giacomo B Marino, Daniel J B Clarke, Eden Z Deng, Avi Ma'ayan
The Gene Expression Omnibus (GEO) is a major open biomedical research repository for transcriptomics and other omics datasets. It currently contains millions of gene expression samples from tens of thousands of studies collected by many biomedical research laboratories from around the world. While users of the GEO repository can search the metadata describing studies for locating relevant datasets, there are currently no methods or resources that facilitate global search of GEO at the data level. To address this shortcoming, we developed RummaGEO, a webserver application that enables gene expression signature search of a large collection of human and mouse RNA-seq studies deposited into GEO...
April 13, 2024: bioRxiv
#32
JOURNAL ARTICLE
Ottavia De Simoni, Melania Scarpa, Ignazio Castagliuolo, Astghik Stepanyan, Imerio Angriman, Andromachi Kotsafti, Camilla Nacci, Federico Scognamiglio, Silvia Negro, Antonella D'Angelo, Valentina Chiminazzo, Gianluca Businello, Cesare Ruffolo, Roberta Salmaso, Boris Franzato, Mario Gruppo, Pierluigi Pilati, Antonio Scapinello, Anna Pozza, Tommaso Stecca, Marco Massani, Ivana Cataldo, Stefano Brignola, Angelo Paolo Dei Tos, Carlotta Ceccon, Vincenza Guzzardo, Chiara Vignotto, Luca Facci, Isacco Maretto, Marco Agostini, Francesco Marchegiani, Giulia Becherucci, Maurizio Zizzo, Giovanni Bordignon, Roberto Merenda, Giovanni Pirozzolo, Alfonso Recordare, Giulia Pozza, Mario Godina, Isabella Mondi, Daunia Verdi, Corrado Da Lio, Licia Laurino, Luca Saadeh, Giorgio Rivella, Silvio Guerriero, Chiara Romiti, Giuseppe Portale, Chiara Cipollari, Ylenia Camilla Spolverato, Giulia Noaro, Roberto Cola, Salvatore Candioli, Laura Gavagna, Fabio Ricagna, Monica Ortenzi, Mario Guerrieri, Giovanni Tagliente, Monica Tomassi, Umberto Tedeschi, Beatrice Salmaso, Gianluca Buzzi, Dario Parini, Daniela Prando, Matteo Zuin, Francesca Bergamo, Vittorina Zagonel, Andrea Porzionato, Francesco Cavallin, Barbara Di Camillo, Loretta Di Cristoforo, Quoc Riccardo Bao, Salvatore Pucciarelli, Romeo Bardini, Gaya Spolverato, Matteo Fassan, Marco Scarpa
BACKGROUND: Long-term daily use of aspirin reduces incidence and mortality due to colorectal cancer (CRC). This study aimed to analyze the effect of aspirin on the tumor microenvironment, systemic immunity, and on the healthy mucosa surrounding cancer. METHODS: Patients with a diagnosis of CRC operated on from 2015 to 2019 were retrospectively analyzed (METACCRE cohort). Expression of mRNA of immune surveillance-related genes (PD-L1, CD80, CD86, HLA I, and HLA II) in CRC primary cells treated with aspirin were extracted from Gene Expression Omnibus-deposited public database (GSE76583)...
April 22, 2024: Cancer
#33
JOURNAL ARTICLE
Hongyan Shi, Caixia Zhou, Yaoyao Zhao
OBJECTIVES: We aimed to establish a diagnostic model of endometriosis (EM) based on disulfidptosis-related genes (DRGs). MATERIALS AND METHODS: The mRNA expression data of EM were downloaded from the gene expression omnibus database and subjected to differential analysis, and co-expression analysis was performed based on 10 disulfidptosis genes to acquire DRGs. The differentially expressed DRGs were subjected to biofunctional analysis. Lasso analysis and support vector machine-recursive feature elimination (SVM-RFE) analysis were employed to extract the intersection of feature genes as biomarkers, and the diagnostic values of biomarkers for EM were evaluated based on receiver operating characteristic curves...
April 21, 2024: Journal of Obstetrics and Gynaecology Research
#34
JOURNAL ARTICLE
Minyao Zhao, Yue Yu, Zhengyu Song
Uveal melanoma (UVM) is the most common primary tumor in adult human eyes. Costimulatory molecules (CMs) are important in maintaining T cell biological functions and regulating immune responses. To investigate the role of CMs in UVM and exploit prognostic signature by bioinformatics analysis. This study aimed to identify and validate a CMs associated signature and investigate its role in the progression and prognosis of UVM. The expression profile data of training cohort and validation cohort were downloaded from The Cancer Genome Atlas (TCGA) dataset and the Gene Expression Omnibus (GEO) dataset...
April 21, 2024: Scientific Reports
#35
JOURNAL ARTICLE
Fan Yang, Junyi Shen, Zhiming Zhao, Wei Shang, Hui Cai
Rheumatoid arthritis (RA) is a persistent autoimmune condition characterized by synovitis and joint damage. Recent findings suggest a potential link to abnormal lactate metabolism. This study aims to identify lactate metabolism-related genes (LMRGs) in RA and investigate their correlation with the molecular mechanisms of RA immunity. Data on the gene expression profiles of RA synovial tissue samples were acquired from the gene expression omnibus (GEO) database. The RA database was acquired by obtaining the common LMRDEGs, and selecting the gene collection through an SVM model...
April 22, 2024: Scientific Reports
#36
JOURNAL ARTICLE
Liang Ming, Junhui Tang, Feiyu Qin, Yan Qin, Duo Wang, Liuying Huang, Yulin Cao, Zhaohui Huang, Yuan Yin
BACKGROUND: Colorectal cancer (CRC) is a highly heterogeneous malignancy, and patients often have different responses to treatment. In this study, the genetic characteristics related to exosome formation and secretion procedure were used to predict chemoresistance and guide the individualized treatment of patients. METHODS: Firstly, seven microarray datasets in Gene Expression Omnibus (GEO) and RNA-Seq dataset from the Cancer Genome Atlas (TCGA) were used to analysis the transcriptome profiles and associated characteristics of CRC patients...
April 16, 2024: Pathology, Research and Practice
#37
JOURNAL ARTICLE
Xiangmei Xu, Jiamin Zhang, Hongyun Xing, Liying Han, Xiaoming Li, Pengqiang Wu, Jirui Tang, Li Jing, Jie Luo, Jing Luo, Lin Liu
Immune thrombocytopenia (ITP), an acquired autoimmune disease, is characterized by immune-mediated platelet destruction. A biomarker is a biological entity that contributes to disease pathogenesis and reflects disease activity. Metabolic alterations are reported to be associated with the occurrence of various diseases. As metabolic biomarkers for ITP have not been identified. This study aimed to identify metabolism-related differentially expressed genes as potential biomarkers for pathogenesis of ITP using bioinformatic analyses...
April 19, 2024: Scientific Reports
#38
JOURNAL ARTICLE
Weizhen Zhang, Fangfang Huang, Xuexuan Ding, Jingtong Qin, Wenjian Wang, Lianxiang Luo
Ferroptosis is a programmed form of cell death regulated by iron and has been linked to the development of asthma. However, the precise mechanisms driving ferroptosis in asthma remain elusive. To gain deeper insights, we conducted an analysis of nasal epithelial and sputum samples from the GEO database using three machine learning methods. Our investigation identified a pivotal gene, Arachidonate 15-lipoxygenase (ALOX15), associated with ferroptosis in asthma. Through both in vitro and in vivo experiments, we further confirmed the significant role of ALOX15 in ferroptosis in asthma...
April 18, 2024: Biochimica et Biophysica Acta. Molecular Basis of Disease
#39
JOURNAL ARTICLE
Junbo Zhang, Yongbin Di, Bohao Zhang, Tianke Li, Dan Li, Haolei Zhang
Oral squamous cell carcinoma (OSCC) is a malignant tumor that occurs in oral cavity and is dominated by squamous cells. The relationship between CDK1, CCNA2, and OSCC is still unclear. The OSCC datasets GSE74530 and GSE85195 configuration files were downloaded from the Gene Expression Omnibus (GEO) database and were derived from platforms GPL570 and GPL6480. Differentially expressed genes (DEGs) were screened. The weighted gene co-expression network analysis, functional enrichment analysis, gene set enrichment analysis, construction and analysis of protein-protein interaction (PPI) network, Comparative Toxicogenomics Database analysis were performed...
April 19, 2024: Medicine (Baltimore)
#40
JOURNAL ARTICLE
Ning Cao, Ziwei Wan, Donghui Chen, Li Tang
Early diagnosis of peri-implantitis (PI) is crucial to understand its pathological progression and prevention. This study is committed to investigating the signature genes, relevant signaling pathways and their associations with immune cells in PI. We analyzed differentially expressed genes (DEGs) from a PI dataset in the gene expression omnibus database. Functional enrichment analysis was conducted for these DEGs. Weighted Gene Co-expression Network Analysis was used to identify specific modules. Least absolute shrinkage and selection operator and support vector machine recursive feature elimination were ultimately applied to identify the signature genes...
April 19, 2024: Medicine (Baltimore)
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