Developing the new diagnostic model by integrating bioinformatics and machine learning for osteoarthritis by Jian Du, Tian Zhou, Wei Zhang, Wei Peng

“…Methods From the Gene Expression Omnibus (GEO) database, we first obtained OA synovial tissue microarray datasets. Differentially expressed genes (DEGs) associated with OA were identified through utilization of the Limma package and weighted gene co-expression network analysis (WGCNA). …”
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Myogenic IGFBP5 levels in rhabdomyosarcoma are nourished by mesenchymal stromal cells and regulate growth arrest and apoptosis by Yue Zhang, Karim Katkhada, Liu Zhen Meng, Binbin Zhao, Shanlin Tong, Wiem Chaabane, Aditi Kallai, Nicholas P. Tobin, Arne Östman, Alessandro Mega, Monika Ehnman

“…These effects were lost when the stromal cells were exposed to RMS cells, either short-term in vitro, or long-term in hindlimb muscle in vivo. High resolution microarray-based Clariom D gene expression analysis identified insulin-like growth factor binding protein 5 (IGFBP5) as the top upregulated gene in RMS cells exposed to naïve stromal cells, and effects on growth arrest, caspase 3/7 activation, and myogenic cell identity were demonstrated in functional assays. …”
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A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. by Katherine James, Shereen Al-Ali, Jessica Tarn, Simon J Cockell, Colin S Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin T Pease, Paul Emery, Peter Lanyon, John A Hunter, Monica Gupta, Michele Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, UK Primary Sjögren’s Syndrome registry, Anil Wipat, Julia Newton, David E Jones, John Isaacs, Jennifer Hallinan, Wan-Fai Ng

“…<h4>Methods</h4>Whole blood samples from 133 fully-phenotyped pSS patients stratified for the presence of fatigue, collected by the UK primary Sjögren's Syndrome Registry, were used for whole genome microarray. The resulting data were analysed both on a gene by gene basis and using pre-defined groups of genes. …”
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Screening and identification of potential target of 1′-acetoxychavicol acetate (ACA) in acquired lapatinib-resistant breast cancer by Febri Wulandari, Ahmad Fauzi, Muhammad Da'i, Mahmoud Mirzaei, Maryati, Kun Harismah

“…We identified differentially expressed genes (DEGs) using GSE16179 microarray data. DEGs from ACA-treated and lapatinib-resistant cells were analyses using Panther DB, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and protein-protein interaction (PPI) network analysis. …”
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PM2.5 Exposure in the Respiratory System Induces Distinct Inflammatory Signaling in the Lung and the Liver of Mice by Soi Jeong, Sang A Park, Inwon Park, Pilhan Kim, Nam Hoon Cho, Jin Won Hyun, Young-Min Hyun

“…We then conducted mRNA microarray analysis to further observe how PM2.5 affects gene expression patterns in the lung and the liver. …”
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MicroRNA let-7f protects against H2O2-induced oxidative damage in neuroblastoma cells by targeting AKT-2 by Kuo Li, Zhan-Qiang Wang, Jun-Ling Zhang, Pei-Yuan Lv

“…Material and methods miRNA microarray analysis was performed to detect the miRNAs’ differential expression in AD patients and normal elderly volunteers. …”
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The potential radiosensitization target PFKFB3 is related to response to radiotherapy in SweBCG91RT: a randomized clinical trial with long-term follow-up by Moa Egelberg, Tommaso De Marchi, Niklas Schultz, Lena Tran, Per Karlsson, Erik Holmberg, Gyula Pekar, Fredrika Killander, Emma Niméus

“…Methods Nuclear protein levels of PFKFB3 were assessed with immunohistochemistry in primary breast tumors (n = 970) and whole-cell RNA levels with microarray gene expression (n = 765). Multivariable competing risks regression analysis was employed for the effect of radiotherapy on incidence of ipsilateral breast tumor recurrence (IBTR), depending on PFKFB3 levels. …”
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L-serine-O-sulfate alters cellular ultrastructure and mitigates the capacity of biofilm formation in Streptococcus mutans UA159 via interfering with glutamate racemase by Jianying Zhang, He-Ling Wang, Tianyu Ding, Yingjie Sun, Shaotai Wang, Chengcheng Yin

“…Biofilm formation was severely impaired, with 63 % reduction in biomass and significant disruption of extracellular matrix integrity. Microarray-based gene expression analysis identified 119 differentially expressed genes, predominantly downregulated (111/119), affecting translation machinery, metabolic pathways, and transmembrane transport. …”
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Identification of metabolism-related key genes as potential biomarkers for pathogenesis of immune thrombocytopenia by Xiangmei Xu, Jiamin Zhang, Hongyun Xing, Liying Han, Xiaoming Li, Pengqiang Wu, Jirui Tang, Li Jing, Jie Luo, Jing Luo, Lin Liu

“…This study aimed to identify metabolism-related differentially expressed genes as potential biomarkers for pathogenesis of ITP using bioinformatic analyses.The microarray expression data of the peripheral blood mononuclear cells were downloaded from the Gene Expression Omnibus database (GSE112278 download link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?…”
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Peroxisome proliferator‐activated receptor gamma (PPARγ) regulates lactase expression and activity in the gut by Mathurin Fumery, Silvia Speca, Audrey Langlois, Anne‐Marie Davila, Caroline Dubuquoy, Marta Grauso, Anthony Martin Mena, Martin Figeac, Daniel Metzger, Christel Rousseaux, Jean‐Frederic Colombel, Laurent Dubuquoy, Pierre Desreumaux, Benjamin Bertin

“…This study aims at characterizing PPARγ target genes involved in intestinal metabolic functions. In microarray analysis, the LCT gene was the most upregulated by PPARγ agonists in Caco‐2 cells. …”
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Over Time Changes in the Transcriptomic Profiles of Tomato Plants with or Without <i>Mi-1</i> Gene During Their Incompatible or Compatible Interactions with the Whitefly <i>Bemisia... by Susana Pascual, Clara I. Rodríguez-Álvarez, Irene López-Vidriero, José M. Franco-Zorrilla, Gloria Nombela

“…Motelle, incompatible interaction) was studied using the oligonucleotide microarray technique. Both interactions were studied 2 and 12 days post infestation (dpi) of plants with adult insects. …”
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Critical gene network and signaling pathway analysis of the extracellular signal-regulated kinase (ERK) pathway in ischemic stroke by Rui Mao, Lei Wang, Haitao Zhang, Jiaojiao Gong, Hua Liu

“…We sought to integrate multiple ischemic stroke transcriptomic datasets, identify key extracellular signal-regulated kinase (ERK) pathway–related biomarkers, delineate immune–stromal heterogeneity, and develop a nomogram for clinical risk assessment.MethodsWe retrieved three public microarray datasets (GSE22255, GSE16561, GSE58294) and merged two of them (GSE22255, GSE16561) into a discovery cohort after stringent batch correction. …”
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Transcriptomic Deconvolution in Acute Myocardial Infarction: Exploring Diagnostic Potential and Validation Through Blood Counts by Murilo de Queiroz Ramos, José Victor Almeida Guimarães, Diego Moura Tanajura, Kiyoshi Ferreira Fukutani, Hanjia Gao

“…To validate the findings, neutrophil and lymphocyte counts were obtained from blood counts and correlated with creatine kinase-MB levels in 22 patients with AMI from Hospital Geral Roberto Santos. Results:. Two microarray datasets from the Gene Expression Omnibus database were analyzed, containing a total of 31 eligible blood transcriptome samples. …”
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The role of p53-microRNA 200-Moesin axis in invasion and drug resistance of breast cancer cells by Farheen Alam, Fatima Mezhal, Hussain EL Hasasna, Vidhya A Nair, SR Aravind, Maha Saber Ayad, Ahmed El-Serafi, Wael M Abdel-Rahman

“…MicroRNA expression was analyzed using microarray analysis and confirmed by real-time polymerase chain reaction. …”
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Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS). by Laura E Cox, Laura Ferraiuolo, Emily F Goodall, Paul R Heath, Adrian Higginbottom, Heather Mortiboys, Hannah C Hollinger, Judith A Hartley, Alice Brockington, Christine E Burness, Karen E Morrison, Stephen B Wharton, Andrew J Grierson, Paul G Ince, Janine Kirby, Pamela J Shaw

“…Only one had a recognised family history of ALS and none had clinically apparent dementia. Microarray analysis of motor neurons from CHMP2B cases, compared to controls, showed a distinct gene expression signature with significant differential expression predicting disassembly of cell structure; increased calcium concentration in the ER lumen; decrease in the availability of ATP; down-regulation of the classical and p38 MAPK signalling pathways, reduction in autophagy initiation and a global repression of translation. …”
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Uncovering genetic contributors to developmental delay and intellectual disability: a focus on CNVs in pediatric patients by Yilun Tao, Yilun Tao, Hongzhi Guo, Dong Han, Miao Yang, Ting Lun, Lihong Wang, Wenxia Song, Haiwei Wang, Xiaoze Li

“…BackgroundDevelopmental delay (DD) and intellectual disability (ID) are prevalent in children and often have genetic causes, particularly copy number variations (CNVs). Chromosomal microarray analysis (CMA) and whole-exome sequencing (WES) are key diagnostic tools for identifying genetic contributions to these disorders. …”
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Identification of GBP6 as a potential prognostic biomarker in esophageal carcinoma by integrated bioinformatics analysis and experiment validation by Shilin Fang, Yang Ding, Yifan Jia, Liping Gao, Yumei Ning, Guifang Wu, Jun Fang, Yongxi Zhang, Haizhou Wang, Hengning Ke

“…Immunohistochemistry was used to validate the results in an ESCA tissue microarray. The proliferative activity of ESCA cells was evaluated using cell counting kit 8 assay. …”
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Bioinformatics Identification and Validation of Ferroptosis-Related Key Genes and Therapeutic Compounds in Septic Lung Injury by Li Z, Gan H, Li S, Xue Y, Luo K, Huang K, Zhang Y, Wang Y, Jiang L, Zhang H

“…This study aimed to elucidate and validate key ferroptosis-related genes involved in the pathogenesis of SLI through bioinformatics analysis and experimental validation.Methods: Microarray data related to SLI from the GSE130936 dataset were downloaded from the Gene Expression Omnibus (GEO) database. …”
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Bioinformatic analyses reveal lysosomal-associated protein transmembrane 5 as a potential therapeutic target in lipotoxicity-induced injury in diabetic kidney disease by Xin Chen, Shenglong Zhu, Ciyou Huang, Jiayi Liu, Jinbang Wang, Siyuan Cui

“…Here, we analyzed the GSE 30529 microarray datasets of human tubulointerstitial tissue samples from the Gene Expression Omnibus database (GEO). …”
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Mapping autoantibody targets of full-length C-reactive protein in systemic lupus erythematosus: importance for neutrophil function and classical complement activation by Jesper Karlsson, Lina Wirestam, Hanna Duàn, Suhana Ahmad, Daniel Appelgren, Helena Enocsson, Jonas Wetterö, Christopher Sjöwall

“…The levels of anti-CRP and SLE-associated antibodies were assessed, and a microarray-based linear epitope mapping was performed to detect binding sites on the full CRP monomer. …”
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