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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Hepatic Gene Expression Profiles Are Altered by Dietary Unsalted Korean Fermented Soybean (Chongkukjang) Consumption in Mice with Diet-Induced Obesity by JuRyoun Soh, Dae Young Kwon, Youn-Soo Cha

“…We found that Chongkukjang, traditional unsalted fermented soybean, has an antiobesity effect in mice with diet-induced obesity and examined the changes in hepatic transcriptional profiles using cDNA microarray. …”
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AssayBLAST: A Bioinformatic Tool for <i>In Silico</i> Analysis of Molecular Multiparameter Assays by Maximilian Collatz, Sascha D. Braun, Martin Reinicke, Elke Müller, Stefan Monecke, Ralf Ehricht

“…This high accuracy demonstrates the method’s effectiveness in reliably using BLAST hits and mismatch counts to predict microarray results. …”
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A systems biology approach to prediction of oncogenes and molecular perturbation targets in B‐cell lymphomas by Kartik M Mani, Celine Lefebvre, Kai Wang, Wei Keat Lim, Katia Basso, Riccardo Dalla‐Favera, Andrea Califano

“…Such a strategy provides important insights into tumorigenesis, effectively extending and complementing existing methods. …”
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Integrative analysis of co-expression networks and codon usage bias in maize under biotic stress. by Zahra Zinati, Leyla Nazari

“…Understanding the complex networks underlying the biotic stress response in maize is crucial for developing effective approaches to improve tolerance. We identified 1449 differentially expressed genes (DEGs) by meta-analysis of the public microarray gene expression profile. …”
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c-Triadem: A constrained, explainable deep learning model to identify novel biomarkers in Alzheimer's disease. by Sherlyn Jemimah, Ferial Abuhantash, Aamna AlShehhi

“…We trained the model with blood genotyping data, microarray, and clinical features from the Alzheimer's Neuroimaging Disease Initiative (ADNI). …”
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Tumor immune microenvironment permissive to metastatic progression of ING4-deficient breast cancer. by Emily Tsutsumi, Anne M Macy, Janine LoBello, Karen T Hastings, Suwon Kim

“…To characterize the tumor immune microenvironment associated with ING4-deficient tumors, three approaches were employed in this study: First, tissue microarrays composed of 246 primary breast tumors including 97 ING4-deficient tumors were evaluated for the presence of selective immune markers, CD68, CD4, CD8, and PD-1, using immunohistochemical staining. …”
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Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis. by Venkata Suresh Bonthala, Katie Mayes, Joanna Moreton, Martin Blythe, Victoria Wright, Sean Tobias May, Festo Massawe, Sean Mayes, Jamie Twycross

“…Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. …”
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Cell cycle- and cancer-associated gene networks activated by Dsg2: evidence of cystatin A deregulation and a potential role in cell-cell adhesion. by Abhilasha Gupta, Daniela Nitoiu, Donna Brennan-Crispi, Sankar Addya, Natalia A Riobo, David P Kelsell, Mỹ G Mahoney

“…CSTA is deregulated in several skin cancers, including squamous cell carcinomas (SCC) and loss of function mutations lead to recessive skin fragility disorders. The microarray results were confirmed by qPCR, immunoblotting, and immunohistochemistry. …”
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Identification of Potential Therapeutic Targets in the Liver of Pioglitazone-Treated Type 2 Diabetes Sprague-Dawley Rats via Expression Profile Chip and iTRAQ Assay by Zhong-Xia Lu, Wen-Jun Xu, Yang-Sheng Wu, Chang-Yu Li, Yi-Tao Chen

“…After treatment with pioglitazone for 11 weeks, the effects on fasting blood glucose, body weight, and blood biochemistry parameters were evaluated. …”
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Molecular characterization of adipose tissue in the African elephant (Loxodonta africana). by Emeli M Nilsson, Hernan P Fainberg, Siew S Choong, Thomas C Giles, James Sells, Sean May, Fiona J Stansfield, William R Allen, Richard D Emes, Alison Mostyn, Nigel P Mongan, Lisa Yon

“…RNA was extracted and histological sections created and analyzed by microarray, PCR and immunohistochemistry respectively. …”
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miRNA-REGULATED PATHWAYS OF CD8+ T CELLS IN TNBC MOUSE MODEL by Müge Öçal Demirtaş, Bala Gür Dedeoğlu

“…Following RNA isolation, miRNA microarray analysis was performed. Differentially expressed miRNAs between the groups were detected. …”
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Long-term expansion of basal cells and the novel differentiation methods identify mechanisms for switching Claudin expression in normal epithelia by Akihito Inoko, Norihito Soga, Minako Suzuki, Tohru Kiyono, Junichi Ikenouchi, Takahiro Kojima, Yoshikatsu Sato, Daisuke Saito, Tatsuo Miyamoto, Naoki Goshima, Hideaki Ito, Kenji Kasai

“…To verify this differentiation-switching technique, we obtained microarray data comparing each differentiation state. …”
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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 changes during hepatic ischemia-reperfusion in the rat. by Valerie Zabala, Joan M Boylan, Paul Thevenot, Anderson Frank, Dewahar Senthoor, Varun Iyengar, Hannah Kim, Ari Cohen, Philip A Gruppuso, Jennifer A Sanders

“…There are few effective targeted strategies to reduce hepatic ischemia-reperfusion (IR) injury, a contributor to poor outcomes in liver transplantation recipients. …”
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Expression and Promoter Analysis of Six Heat Stress-Inducible Genes in Rice by Wirat Rerksiri, Xianwen Zhang, Hairong Xiong, Xinbo Chen

“…Six highly heat responsive genes were identified in rice by microarray data analysis. The qRT-PCR analysis confirmed that the expression of these six genes were highly heat inducible and moderately responded to salt stress, polyethylene glycol, and abscisic acid treatment, but little affected by cold treatment. …”
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Comprehensive analysis of intervention and control studies for the computational identification of dengue biomarker genes. by Jibon Kumar Paul, Mahir Azmal, Tasnim Alam, Omar Faruk Talukder, Ajit Ghosh

“…Despite significant progress in understanding Dengue fever, effective prognosis and treatment remain elusive due to the complex clinical presentations and limitations in current diagnostic methods. …”
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Upregulated interleukin‐6 expression contributes to erlotinib resistance in head and neck squamous cell carcinoma by Aditya Stanam, Laurie Love-Homan, Tisha S. Joseph, Madelyn Espinosa-Cotton, Andrean L. Simons

“…Mechanisms of acquired resistance to the EGFR TKI erlotinib was investigated by developing erlotinib‐resistant HNSCC cell lines and comparing their gene expression profiles with their parental erlotinib‐sensitive HNSCC cell lines using microarray analyses and subsequent pathway and network analyses. …”
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Potential application of the bulk RNA sequencing in routine MPN clinics by Shenglong Li, Sanyun Wu, Mingli Xu, Xuedong Li, Xuelan Zuo, Yingying Wang

“…Additionally, data from the microarray datasets [GSE26049, GSE2191] were included in this study. …”
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Mutation Spectrum of the ABCA4 Gene in a Greek Cohort with Stargardt Disease: Identification of Novel Mutations and Evidence of Three Prevalent Mutated Alleles by Kamakari Smaragda, Kokkinou Vassiliki, Koutsodontis George, Stamatiou Polixeni, Giatzakis Christoforos, Anastasakis Anastasios, Aslanides Ioannis Minas, Koukoula Stavrenia, Panagiotoglou Theoni, Datseris Ioannis, Tsilimbaris K. Miltiadis

“…A total of 59 patients were analyzed for ABCA4 mutations using the ABCR400 microarray and PCR-based sequencing of all coding exons and flanking intronic regions. …”
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