Bioinformatics methods for identifying differentially expressed genes and signaling pathways in nano-silica stimulated macrophages by Lin Zhang, Changfu Hao, Juan Li, Yaqian Qu, Lei Bao, Yiping Li, Zhongzheng Yue, Miao Zhang, Xinghao Yu, Huiting Chen, Jianhui Zhang, Di Wang, Wu Yao

“…The incidence of disease relating to nanoparticle exposure has been rising rapidly in recent years, for which there is no effective treatment. Macrophage is suggested to play a crucial role in the development of pulmonary disease. …”
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Expression profiles and bioinformatic analysis of circular RNA in rheumatic heart disease: potential hsa_circ_0001490 and hsa_circ_0001296 as a diagnostic biomarker by Xiaoliang Chen, Lina Chen, Li Bi, Shunying Zhao, Xiaoyan Hu, Ni Li, Linwen Zhu, Guofeng Shao

“…The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to predict the potential functions of the differentially expressed genes and RHD-related pathways.ResultsFour circRNAs were selected from circRNA microarray data. qRT-PCR confirmed that hsa_circ_0001490 and hsa_circ_0001296 were significantly upregulated in RHD plasma (4.28-fold, P < 0.001; 5.24-fold, P < 0.001, respectively). …”
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c-Myc-dependent LAMP3 regulates the proliferation, metastasis and metabolic reprogramming of tongue squamous cell carcinoma by Jing Feng, Wei He, Jin Fang

“…Differential expression of LAMP3 in TSCC from GEO microarray was analyzed, and pathway enrichment analysis of LAMP3 was performed utilizing GSEA. …”
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Exosomal circRNA-0008302 from Adipose-derived Stem Cells Protects Against Myocardial Injury by Chengyan Hu, Shuai Wang, Yanling Wang, Zhenxing Fan, Xipeng Sun, Zhi Liu

“…The expression levels of miR-466i-5p were evaluated, and western blotting was performed to detect the expression of methionine sulfoxide reductase A (MsrA) protein. …”
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General Approach to Identifying Potential Targets for Cancer Imaging by Integrated Bioinformatics Analysis of Publicly Available Genomic Profiles by Yongliang Yang, S. James Adelstein, Amin I. Kassis

“…Here we present a simple and integrated bioinformatics analysis approach that assembles a public cancer microarray database with a pathway knowledge base for ascertaining and prioritizing upregulated genes encoding cell surface- or membrane-bound proteins, which could serve imaging targets. …”
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CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes. by Rebecca Casaday Potts, Peisu Zhang, Andrea L Wurster, Patricia Precht, Mohamed R Mughal, William H Wood, Yonqing Zhang, Kevin G Becker, Mark P Mattson, Michael J Pazin

“…CHD5 protein was predominantly nuclear in primary rat neurons and brain sections. Microarray analysis revealed genes that were upregulated and downregulated when CHD5 was depleted from primary neurons. …”
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Identification and validation of TSPAN13 as a novel temozolomide resistance-related gene prognostic biomarker in glioblastoma. by Haofei Wang, Zhen Liu, Zesheng Peng, Peng Lv, Peng Fu, Xiaobing Jiang

“…Using LASSO Cox analysis, we selected 12 TMZR-RDEGs to construct a risk score model, which was evaluated for performance through survival analysis, time-dependent ROC, and stratified analyses. …”
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Have maternal or paternal ages any impact on the prenatal incidence of genomic copy number variants associated with fetal structural anomalies? by Marta Larroya, Marta Tortajada, Eduard Mensión, Montse Pauta, Laia Rodriguez-Revenga, Antoni Borrell

“…We conducted a non-paired case-control study (1:2 ratio) among pregnancies undergoing chromosomal microarray analysis (CMA) because of fetal ultrasound anomalies, from December 2012 to May 2020. …”
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Apoptosis-associated genetic mechanisms in the transition from rheumatoid arthritis to osteoporosis: A bioinformatics and functional analysis approach by Hao-Ju Lo, Chun-Hao Tsai, Tsan-Wen Huang

“…This study explores the mechanisms of glucocorticoid-induced osteoporosis (OP) and Rheumatoid arthritis (RA), focusing on apoptosis and its role in the progression from RA to OP. Using microarray data from the GEO database, differential gene expression analysis was conducted with the limma package, identifying significant genes in RA and OP. …”
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Cuproptosis genes in predicting the occurrence of allergic rhinitis and pharmacological treatment. by Ting Yi

“…<h4>Results</h4>Four AR signature genes (MRPS30, CLPX, MRPL13, and MRPL53) were selected by the MCC, EPC, BottleNeck, and Closeness algorithms. …”
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SMART: unique splitting-while-merging framework for gene clustering. by Rui Fa, David J Roberts, Asoke K Nandi

“…Moreover, two real microarray gene expression datasets are studied using this approach. …”
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Bioinformatic-based differential expression gene expressions of epithelial mesenchymal transformation in diabetic kidney disease and prediction of traditional Chinese medicine by Liu Wu, Zhou Yi, Yu Fang-ning, Zhang Ning

“…ObjectiveBased upon the bioinformatic analysis of gene chip data between patients with diabetic kidney disease （DKD） and normal controls， differentially expressed genes of epithelial mesenchymal transformation of DKD were screened for elucidating its pathogenesis and predicting the potential therapeutic Chinese medicine for DKD.MethodsGSE23338 microarray data were downloaded from gene expression omnibus， related differentially expressed genes screened by R language and differentially expressed genes analyzed by Gene Ontology， Kyoto Encyclopedia of Genes and Genomes. …”
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Cellular senescence-associated genes in rheumatoid arthritis: Identification and functional analysis. by You Ao, Qing Lan, Tianhua Yu, Zhichao Wang, Jing Zhang

“…In our study, we analyzed RA microarray data from the Gene Expression Omnibus (GEO) and focused on cellular senescence genes from the CellAge database. …”
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Ultradian cortisol pulsatility encodes a distinct, biologically important signal. by Andrew McMaster, Maryam Jangani, Paula Sommer, Namshik Han, Andy Brass, Stephen Beesley, Weiqun Lu, Andrew Berry, Andrew Loudon, Rachelle Donn, David W Ray

“…In addition, effects on glucocorticoid receptor (GR) expression levels and phosphorylation, as a potential mediator, were measured.…”
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Electrochemical Strategies for MicroRNA Quantification Leveraging Amplification and Nanomaterials: A Review by Alexander Hunt, Gymama Slaughter

“…However, conventional detection methods, such as Northern blotting, RT-PCR, and microarrays, are limited by low sensitivity, lengthy protocols, and limited specificity. …”
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DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. by Shaun Mahony, Philip E Auron, Panayiotis V Benos

“…Prediction of the identity or the structural class of a protein that binds to a given DNA pattern will enhance the analysis of microarray and ChIP-chip data where frequently multiple putative targets of usually unknown TFs are predicted. …”
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Stabilization of Transcription Factor, HIF-1α by Prolylhydroxylase 1 Knockout Reduces Cardiac Injury After Myocardial Infarction in Mice by Mahesh Thirunavukkarasu, Seetur R. Pradeep, Babatunde Oriowo, Sue Ting Lim, Monica Maloney, Shayan Ahmed, Nicole Taylor, David M. Russell, Pavayee Socrates, Ethan Batko, Matan Berkovsky, John Alexander Palesty, Nilanjana Maulik

“…Our current work investigates the protective effects of PHD1 knockout in mice against myocardial infarction. …”
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Exploration of autophagy-related molecular mechanisms underlying epilepsy using multiple datasets by Yongfei Wang, Haoxuan Zeng, Chongxu Liu, Jianjun Chen, Yihong Huang, Xianju Zhou

“…Methods We analyzed GSE143272 and GSE4290 microarray datasets from the NCBI Gene Expression Omnibus database, which is established based on evaluations of peripheral blood samples. …”
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Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas by Xueren Gao, Jianguo Wang, Shulong Zhang

“…The aim of the present study was to identify hub genes and pathways in ATC by microarray expression profiling. Two independent datasets (GSE27155 and GSE53072) were downloaded from GEO database. …”
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Hub genes and associated drugs for multiple myeloma with 1q21+: identified by bioinformatic analysis by Zhiqiang Xu, Jieni Yu, Yamei Chen

“…While 1q21+ was common genetic alteration and found to have adverse effect on prognosis, the underlying genes remain unclear. …”
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