Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective by Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Sandra Romero-Hidalgo, Alonso A. Lopez-Zavala, Andrés Cota-Huízar, Melany Cervantes-Echeverría, Rogerio R. Sotelo-Mundo, Adrian Ochoa-Leyva

“…Results Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. …”
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Profiling of gastric cancer cell-surface markers to achieve tumour–normal discrimination by Henry Yang, Khek Yu Ho, Judith Toh, Michal Marek Hoppe, Teena Thakur, Kar Tong Tan, Brendan Pang, Sharmaine Ho, Rony Roy, Khay Guan Yeoh, Raghav Sundar, Anand Jeyasekharan

“…Promising candidates from this analysis were validated orthogonally using multispectral immunohistochemistry (mIHC) with automated quantitative analysis using the Vectra platform. mIHC was performed on a tissue microarray containing matched normal, marginal and tumour tissues. …”
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Expression of Genes Related to Germ Cell Lineage and Pluripotency in Single Cells and Colonies of Human Adult Germ Stem Cells by Sabine Conrad, Hossein Azizi, Maryam Hatami, Mikael Kubista, Michael Bonin, Jörg Hennenlotter, Karl-Dietrich Sievert, Thomas Skutella

“…Genome-wide comparisons with microarray analysis confirmed that different haGSC colonies exhibited gene expression heterogeneity with more or less pluripotency. …”
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Prevention of hypovolemic circulatory collapse by IL-6 activated Stat3. by Jeffrey A Alten, Ana Moran, Anna I Tsimelzon, Mary-Ann A Mastrangelo, Susan G Hilsenbeck, Valeria Poli, David J Tweardy

“…Pre-treatment of rats with a selective inhibitor of Stat3, T40214, reduced the IL-6-mediated increase in cardiac Stat3 activity, blocked successful resuscitation by IL-6 and reversed IL-6-mediated protection from cardiac apoptosis. …”
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Transcriptional Profile of Kidney from Type 2 Diabetic db/db Mice by Haojun Zhang, Tingting Zhao, Zhiguo Li, Meihua Yan, Hailing Zhao, Bin Zhu, Ping Li

“…We explored changes in the transcriptional profile in spontaneous type 2 diabetic db/db mice by using the cDNA microarray. Compared with control db/m mice, the db/db mice exhibited marked increases in body weight, kidney weight, and urinary albumin excretion. …”
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Long Noncoding RNAs and mRNA Regulation in Peripheral Blood Mononuclear Cells of Patients with Chronic Obstructive Pulmonary Disease by Xiaoyan Qu, Xiaomin Dang, Weijia Wang, Ying Li, Dan Xu, Dong Shang, Ying Chang

“…Methods. lncRNA and mRNA profiling of PBMCs from 17 smokers and 14 COPD subjects was detected by high-throughput microarray. The expression of dysregulated lncRNAs was validated by qPCR. …”
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Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease by Lu-Mei Chi, Li-Ping Wang, Dan Jiao

“…This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. …”
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Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72. by Abhijit Sarkar, Barbara Reinhold-Hurek

“…<h4>Methodology/principal findings</h4>A DNA microarray, comprising 70-mer oligonucleotides representing 3989 open reading frames of the genome of strain BH72, was used for transcriptome studies. …”
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Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation. by Alexandra Dumitriu, Jeanne C Latourelle, Tiffany C Hadzi, Nathan Pankratz, Dan Garza, John P Miller, Jeffery M Vance, Tatiana Foroud, Thomas G Beach, Richard H Myers

“…Single-nucleotide polymorphisms (SNPs) selected from a recent meta-analysis of PD genome-wide association studies (GWAS) were successfully genotyped in 50 out of the 53 microarray brains, allowing a targeted expression-SNP (eSNP) analysis for 52 SNPs associated with PD affection at genome-wide significance and the 189 probes from FoxO1 regulated genes. …”
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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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Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions. by Sergio Rojas-Galeano, Emily Hsieh, Dan Agranoff, Sanjeev Krishna, Delmiro Fernandez-Reyes

“…The resulting variable subsets achieved classification accuracies of 99% on Human African Trypanosomiasis, 91% on Tuberculosis, and 91% on Malaria serum proteomic profiles with fewer than 20% of variables selected. Our method scaled-up to dimensionalities of much higher orders of magnitude as shown with gene expression microarray datasets in which we obtained classification accuracies close to 90% with fewer than 1% of the total number of variables.…”
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Pan-cancer analysis identifies CD155 as a promising target for CAR-T cell therapy by Xiaohong Liu, Yue Sun, Boxu Lin, Hao Xiong, Xinyue Lu, Binghe Tan, Chenglin Zhang, Mingyao Liu, Juliang Qin, Na Zhang, Bing Du

“…Conclusions Our study demonstrates that CD155 is selectively expressed in cancer cells while being rarely detected in normal tissues, and may serve as a promising pan-cancer target for CAR-T therapy. …”
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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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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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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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Differentially expressed miR-3680-5p is associated with parathyroid hormone regulation in peritoneal dialysis patients. by Sohyun Jeong, Jung Mi Oh, Kook-Hwan Oh, In-Wha Kim

“…Total RNA from 15 patients (7 and 8 patients in the low and high iPTH groups, respectively) underwent miRNA microarray analysis, and three differentially upregulated (>2-fold change) miRNAs previously associated with human disease were selected for real-time quantitative PCR (qPCR) analysis. …”
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Prevalence and Diversity of <i>Staphylococcus aureus</i> in Bulk Tank Milk from Community-Based Alpine Dairy Pastures in Tyrol, Austria by Nasrin Ramezanigardaloud, Igor Loncaric, Patrick Mikuni-Mester, Masoumeh Alinaghi, Monika Ehling-Schulz, Johannes Lorenz Khol, Tom Grunert

“…A total of 140 isolates collected from the 94 <i>S. aureus</i>-positive community-based Alpine dairy pastures revealed 33 distinct <i>spa</i> types, with t2953 (<i>n</i> = 33), t529 (<i>n</i> = 12), t267 (<i>n</i> = 11), and t024 (<i>n</i> = 10) being the most common. Selected isolates representing the different <i>spa</i> types were characterised by DNA microarray-based genotyping, multi-locus sequence typing (MLST), and antimicrobial susceptibility testing. …”
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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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MOLECULAR AND GENETIC INSIGHTS OF ROOT-KNOT NEMATODES PATHOGENICITY: A REVIEW by Prabina Bhandari, Anjali Thapa, Anusha Ghimire, Sunil Ojha, Srijana Saud, Sanju Aryal

“…Protein analysis and molecular databases help identify down-regulated and up-regulated genes. Microarray technology can provide large-scale gene expression data on plant-nematode interaction, aiding in understanding nematode selection and feeding site alteration, thereby identifying genes controlling cell differentiation and division. …”
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Analytic approaches to clinical validation of results from preclinical models of glioblastoma: A systematic review. by Beth Fitt, Grace Loy, Edward Christopher, Paul M Brennan, Michael Tin Chung Poon

“…In 14 studies published between 2017 and 2020 using TCGA RNA microarray data that should have the same cohort, the median number of patients was 464.5 (interquartile range 220.5-525). …”
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