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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A Bovine Lymphosarcoma Cell Line Infected with Theileria annulata Exhibits an Irreversible Reconfiguration of Host Cell Gene Expression. by Jane H Kinnaird, William Weir, Zeeshan Durrani, Sreerekha S Pillai, Margaret Baird, Brian R Shiels

“…By using comparative microarray analysis of an uninfected bovine cell line and its Theileria infected counterpart, in conjunction with use of the specific parasitacidal agent, buparvaquone, we have identified a large number of host cell gene expression changes that result from parasite infection. …”
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Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. by Carlos Guerrero-Bosagna, Matthew Settles, Ben Lucker, Michael K Skinner

“…A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. …”
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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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Gene expression alterations in the cerebellum and granule neurons of Cstb(-/-) mouse are associated with early synaptic changes and inflammation. by Tarja Joensuu, Saara Tegelberg, Eva Reinmaa, Mikael Segerstråle, Paula Hakala, Heidi Pehkonen, Esa R Korpi, Jaana Tyynelä, Tomi Taira, Iiris Hovatta, Outi Kopra, Anna-Elina Lehesjoki

“…These results suggest that alterations in GABAergic signaling could result in reduced inhibition in Cstb(-/-) cerebellum leading to the hyperexcitable phenotype of Cstb(-/-) mice. At P30, the microarray data revealed a marked upregulation of immune and defense response genes, compatible with the previously reported early glial activation that precedes neuronal degeneration. …”
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Diagnosis of Coronary Heart Diseases Using Gene Expression Profiling; Stable Coronary Artery Disease, Cardiac Ischemia with and without Myocardial Necrosis. by Nabila Kazmi, Tom R Gaunt

“…Interestingly it also showed efficacy in discriminating myocardial infarction patients from patients with clinical symptoms of cardiac ischemia but no myocardial necrosis or stable coronary artery disease, despite the influence of batch effects and different microarray gene chips and platforms.…”
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Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action by Sona Pandey, Rui‐Sheng Wang, Liza Wilson, Song Li, Zhixin Zhao, Timothy E Gookin, Sarah M Assmann, Réka Albert

“…Here, we generate and analyze microarray data from guard cells and leaves of G‐protein subunit mutants of the model plant Arabidopsis thaliana, with or without treatment with the stress hormone, abscisic acid. …”
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Comparative Analysis of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells between Preeclampsia and Normal Pregnant Women by Han-Sung Hwang, Yong-Sun Maeng

“…In addition, many senescence-related differentially expressed genes (DEGs) were identified by analysis of microarray gene expression profiles and significantly associated with the Gene Ontology term cell aging. …”
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Exploring the mechanisms of chronic obstructive pulmonary disease and Crohn’s disease: a bioinformatics-based study by Xinxin Zhang, Caiping Liu, Luqian Cao, Hongguang Tang, Haiyun Jiang, Changjing Hu, Xuehong Dong, Feiyang Zhou, Kunming Qin, Qiang Liu, Jinyang Shen, Yue Zhou

“…From the Gene Expression Omnibus (GEO) microarray dataset, 349 common differentially expressed genes (coDEGs) were identified, and 8 shared hub genes were found: CCL2, CXCL1, TLR2, ICAM1, PTPRC, ITGAX, PTGS2, and MMP9, which were vital for immune function and regulation of inflammatory responses. …”
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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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Evaluation of PD-L1 Expression in Tumor Tissue of Patients with Lung Carcinoma and Correlation with Clinical and Demographic Data by Gustavo Dix Junqueira Pinto, Luciano de Souza Viana, Cristovam Scapulatempo Neto, Sérgio Vicente Serrano

“…Collective analysis by Tissue Microarray Assay (TMA) for PD-L1 expression in tumor cells and IICs did not reproduce the findings for separate individual analysis of tumor tissues. …”
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Research on Biological Detection Based on Reflected Light Images of a Porous Silicon Bragg Mirror by Shuangshuang Zhang, Miao Sun, Jianfeng Yang, Zhenhong Jia, Xiaoyi Lv, Xiaohui Huang

“…The method is low-cost, has a short detection time and can be used in the detection of biosensor microarray.…”
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Molecular correlates of social dominance: a novel role for ependymin in aggression. by Lynne U Sneddon, Rupert Schmidt, Yongxiang Fang, Andrew R Cossins

“…We used a custom cDNA microarray to profile brain transcript expression in a model species, the rainbow trout, which forms tractable linear hierarchies. …”
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Identification of MEG3 and MAPK3 as potential therapeutic targets for osteoarthritis through multiomics integration and machine learning by Bing Ma, Xiaoru Wang, Chengfei Xu, Zelin Xu, Fei Zhang, Wendan Cheng

“…Subsequently, differential expression analysis and WGCNA were applied to synovial tissue microarray datasets obtained from the GEO database. …”
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Transcriptomics, Proteomics and Bioinformatics in Atrial Fibrillation: A Descriptive Review by Martina Belfiori, Lisa Lazzari, Melanie Hezzell, Gianni D. Angelini, Tim Dong

“…Different devices for processing RNA and proteomic samples vary from RNA sequencing and microarray to a wide range of mass spectrometry techniques such as Orbitrap, Quadrupole, LC-MS, and hybrid systems. …”
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Combining mitochondrial proteomes and Mendelian randomization to identify novel therapeutic targets for diabetic nephropathy by Yang Liu, Rong Wu, Zhelun Zhou, Junan Zhou, Jiaai Zhang, Xiaoyi Wang

“…To identify the core proteins among them, Mendelian randomization (MR) analysis, microarray data validation, and drug–target interaction analysis were employed. …”
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Interpretable graph Kolmogorov–Arnold networks for multi-cancer classification and biomarker identification using multi-omics data by Fadi Alharbi, Nishant Budhiraja, Aleksandar Vakanski, Boyu Zhang, Murtada K. Elbashir, Harshith Guduru, Mohanad Mohammed

“…The proposed approach combines differential gene expression with DESeq2, Linear Models for Microarray (LIMMA), and Least Absolute Shrinkage and Selection Operator (LASSO) regression to reduce multi-omics data dimensionality while preserving relevant biological features. …”
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Gene expression profiles of human dendritic cells interacting with Aspergillus fumigatus in a bilayer model of the alveolar epithelium/endothelium interface. by Charles Oliver Morton, Mirjam Fliesser, Marcus Dittrich, Tobias Mueller, Ruth Bauer, Susanne Kneitz, William Hope, Thomas Richard Rogers, Hermann Einsele, Juergen Loeffler

“…This microarray data indicated minimal induction of immune gene expression in A549 alveolar epithelial cells in response to germ tubes of A. fumigatus. …”
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Type-2 diabetes epigenetic biomarkers: present status and future directions for global and Indigenous health by Sarah Munns, Sarah Munns, Alex Brown, Alex Brown, Sam Buckberry, Sam Buckberry

“…We critically evaluate previous DNA methylation biomarker studies, particularly those using microarray platforms, and advocate for a shift towards sequencing-based approaches to improve genome-wide coverage. …”
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Transcriptional meta-analysis and immune cell profiles reveal altered neutrophil dynamics in chronic atrial fibrillation by Elijah Stone, Jude Taylor, Amy Li, Craig S. McLachlan

“…We performed a meta-analysis to combine independent microarray and RNA sequencing (RNAseq) datasets for both persistent and permanent AF left atrial tissue. …”
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