Genomic copy number variants: evidence for association with antibody response to anthrax vaccine adsorbed. by Michael I Falola, Howard W Wiener, Nathan E Wineinger, Gary R Cutter, Robert P Kimberly, Jeffrey C Edberg, Donna K Arnett, Richard A Kaslow, Jianming Tang, Sadeep Shrestha

“…Antibodies to protective antigen were measured at week 8 (early response) and week 30 (peak response) using an enzyme-linked immunosorbent assay. We used DNA microarray data (Affymetrix 6.0) and two CNV detection algorithms, hidden markov model (PennCNV) and circular binary segmentation (GeneSpring) to determine CNVs in all individuals. …”
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Potential role of SLC6A3 in neurodevelopmental impairments associated with corpus callosum abnormalities: insights from CNV analysis and clinical phenotyping by Shan-yu Liu, Wei Huang, Hui-lin Ou, Li Wang, Dan-dan Wang, Wei-he Tan, Qin She

“…Methods From January 2021 to July 2023, 13 children with MRI-confirmed CCAs underwent chromosomal microarray analysis (CMA) for CNV detection. We performed bioinformatic analyses (Gene Ontology, STRING network) to identify neurodevelopmental genes within pathogenic CNVs, and clinical follow up assessed neurobehavioral outcomes. …”
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Identification of PECAM1 as a Prognostic Biomarker for Lung Adenocarcinoma by Shih-Sen Lin, Pei-Sung Hsu, Ying-Chu Lin, Jie-Yu You, Yung-Leun Shih, Hung-Chih Lai

“…<b>Methods</b>: We examined three microarray datasets from the Gene Expression Omnibus (GSE10072, GSE33356, and GSE18842) to detect DEGs between tumor and normal lung tissues. …”
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HuoXueJieDu Formula Alleviates Diabetic Retinopathy in Rats by Inhibiting SOCS3-STAT3 and TIMP1-A2M Pathways by Hongliang Wang, Wei Xing, Shijie Tang, Zhenglin Wang, Tiantian Lv, Yan Wu, Shuzhen Guo, Chun Li, Jing Han, Ruixin Zhu, Wei Wang

“…Whole genome expression profiles in rat retinas were examined using microarray technology. Differential gene expression and pathway enrichment analysis were conducted on the microarray data, with validation through real-time PCR and immunohistochemical staining. …”
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Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes by Iftekhar A. Showpnil, Maria E. Hernandez Gonzalez, Swetha Ramadesikan, Mohammad Marhabaie, Allison Daley, Leeran Dublin-Ryan, Matthew T. Pastore, Umamaheswaran Gurusamy, Jesse M. Hunter, Brandon S. Stone, Dennis W. Bartholomew, Kandamurugu Manickam, Anthony R. Miller, Richard K. Wilson, Rolf W. Stottmann, Daniel C. Koboldt

“…Abstract Long-read sequencing can often overcome the deficiencies in routine microarray or short-read technologies in detecting complex genomic rearrangements. …”
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ANALYSIS OF CELLULAR REACTION TO IFN-γ STIMULATION BY A SOFTWARE PACKAGE GeneExpressionAnalyser by A. V. Saetchnikov, M. M. Yatskou, P. V. Nazarov, L. Vallar, V. V. Apanasovich

“…The developed software has a number of advantages over the existing software: it is free, has a simple and intuitive graphical interface, allows to analyze different types of DNA microarrays, contains a set of methods for complete data analysis and performs effec-tive gene annotation for a selected list of genes.…”
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Comparative Study of PPARγ Targets in Human Extravillous and Villous Cytotrophoblasts by Fulin Liu, Christine Rouault, Mickael Guesnon, Wencan Zhu, Karine Clément, Séverine A. Degrelle, Thierry Fournier

“…Visualizations were prepared in Cytoscape. From our microarray data, 139 DEGs were detected in rosiglitazone-treated EVCTs (RT-EVCTs) and 197 DEGs in rosiglitazone-treated VCTs (RT-VCTs). …”
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An Ensemble Classification Method for High-Dimensional Data Using Neighborhood Rough Set by Jing Zhang, Guang Lu, Jiaquan Li, Chuanwen Li

“…Efficient and effective sample classification and feature selection are challenging tasks due to high dimensionality and small sample size of microarray data. …”
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Bayesian weighted random forest for classification of high-dimensional genomics data by Oyebayo Ridwan Olaniran, Mohd Asrul A. Abdullah

“…In addition, BWRCF also has improved predictive and efficiency abilities over selected competing methods.…”
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Fecal carriage of vanB antibiotic resistance gene affects adipose tissue function under vancomycin use by Lars M. M. Vliex, Giang N. Le, Marina Fassarella, Dorien Reijnders, Gijs H. Goossens, Erwin G. Zoetendal, John Penders, Ellen E. Blaak

“…Abdominal subcutaneous adipose tissue (AT) gene expression was assessed using Affymetrix microarray. Gut microbial composition was determined using the Human Intestinal Tract Chip (HITChip) microarray. …”
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The expression levels of CYP3A4 and CYP3A5 serve as potential prognostic biomarkers in lung adenocarcinoma by Mao Qixing, Xu Juqing, Wang Yajing, Dong Gaochao, Xia Wenjie, Shi Run, Wang Anpeng, Xu Lin, Jiang Feng, Wang Jun

“…The expression of CYP3A4, together with CYP3A5, was detected by the chip data from Gene Expression Omnibus datasets and immunohistochemistry staining of the tissue microarray. …”
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Gene Expression Profiling in Organ Transplantation by Osama Ashry Ahmed Gheith

“…However, because microarray analyses are expensive and time consuming and their statistical evaluation is often very difficult, gene expression analysis using the RTPCR method is nowadays recommended. …”
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Expression of RNA-binding motif 10 is associated with advanced tumor stage and malignant behaviors of lung adenocarcinoma cancer cells by Guofang Guan, Ranwei Li, Wenfang Tang, Tiecheng Liu, Zhenzhong Su, Yan Wang, Jingjin Tan, Shan Jiang, Ke Wang

“…Complementary DNA microarray was used to profile RNA-binding motif 10–regulated genes. …”
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Profiling of Circulating Cell-free DNA Methylation Patterns Identifies Aberrant Methylated CTBP1 Promotor Sites for Prediction of Alzheimer’s Disease by Zhiwu Dong, Kewen Zhao, Hongjun Gu, Wenwei Yang, Xin Zhang

“…The R Bioconductor Linear Models for Microarray Data (LIMMA) package was employed to identify methylation variable positions (MVPs), and Probe Lasso was used to pinpoint differentially methylated regions (DMRs) linked to AD. …”
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Hyperuricemia suppresses lumican, exacerbating adverse remodeling after myocardial infarction by promoting fibroblast phenotype transition by Zehao Zhuang, Ao Liu, Jinghong Zhang, Shuangjian Han, Lu Tang, Tingting Yu, Yiping Shi, Hui Li, Heng Yang, Peiyuan Bai, Yanhua Tang

“…We conducted an enzyme-linked immunosorbent assay, histological detection, immunofluorescence, sequencing data processing, single-cell RNA-seq, and functional enrichment analysis. …”
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Targeting PRDX2 to inhibit tumor growth and metastasis in triple-negative breast cancer: the role of FN1 and the PI3K/AKT/SP1 pathway by Jiawei Zhou, Anqi Cheng, Jianqiang Guo, Yafeng Liu, Xuan Li, Maoqian Chen, Dong Hu, Jing Wu

“…Methods This study utilized TNBC tissue microarrays to detect Peroxiredoxin 2 (PRDX2) expression levels and analyzed the correlation between PRDX2 and tumor invasion as well as invasion-related gene expression through the TCGA database. …”
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Identification of Key Biomarkers and Candidate Molecules in Non-Small-Cell Lung Cancer by Integrated Bioinformatics Analysis by Liyan Yu, Xuemei Liang, Jianwei Wang, Guangxiang Ding, Jinhai Tang, Juan Xue, Xin He, Jingxuan Ge, Xianzhang Jin, Zhiyi Yang, Xianwei Li, Hehuan Yao, Hongtao Yin, Wu Liu, Shengchen Yin, Bing Sun, Junxiu Sheng

“…From the Gene Expression Omnibus database, GSE118370 and GSE10072 microarray datasets were obtained. Identifying the differentially expressed genes (DEGs) between lung adenocarcinoma and normal samples was done. …”
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Clinicopathologic implications of Myb and Beta-catenin expression in adenoid cystic carcinoma by Susan Park, Manali Vora, Annemieke van Zante, Joseph Humtsoe, Hyun-Su Kim, Sue Yom, Shweta Agarwal, Patrick Ha

“…In this study, we aim to analyze the impact of Myb and β-catenin expression on prognosis in ACC. Methods A tissue microarray constructed from archival tissue from 64 patients with ACC was stained for Myb and β-catenin; both localization and intensity were evaluated. …”
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M2BPgs-HCC: An Automated Multilectin Bead Array Indicating Aberrant Glycosylation Signatures Toward Hepatitis C Virus-Associated Hepatocellular Carcinoma Prognosis by Hiroko Shimazaki, Haruki Uojima, Kazumi Yamasaki, Tomomi Obayashi, Sayaka Fuseya, Takashi Sato, Masashi Mizokami, Atsushi Kuno

“…Regular monitoring of patients with a history of hepatitis C virus (HCV) infection is critical for the detection and management of hepatocellular carcinoma (HCC). …”
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Unravelling the Impact of an Additional Sex Chromosome in an Adult Female by Sigin George, Vikas Dagar, Barun Kumar Chakrabarty, N. Nagaraja

“…Interphase fluorescence in situ hybridisation was performed to confirm the diagnosis. Chromosomal microarray, which is a more expensive test, substantiated the presence of additional X chromosomes but failed to detect the presence of low level of mosaicism. …”
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