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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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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Transcriptomic profile induced by calcitriol in CaSki human cervical cancer cell line. by Euclides Avila, Luis David Hernández-Monterde, Alberto Cedro-Tanda, Tomas Misael Lizardi-Aguilera, David Barrera, Francisco Vladimir Villegas-Rodriguez, Janice García-Quiroz, Lorenza Díaz, Fernando Larrea

“…We examined the transcriptional changes induced by calcitriol in CaSki cells, a cervical cell line harboring multiple copies of HPV16, the primary causal agent of cervical cancer. Our microarray findings, revealed that calcitriol regulated over 1000 protein-coding genes, exhibiting a predominantly repressive effect on the CaSki cell transcriptome by suppressing twice as many genes as it induced. …”
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The novel long noncoding RNA linc00467 promotes cell survival but is down-regulated by N-Myc. by Bernard Atmadibrata, Pei Y Liu, Nicolas Sokolowski, Lihong Zhang, Matthew Wong, Andrew E Tee, Glenn M Marshall, Tao Liu

“…Moreover, Affymetrix microarray analysis revealed that one of genes significantly up-regulated by linc00467 siRNA was the tumour suppressor gene DKK1. …”
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A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1. by Davide Danovi, Amos Folarin, Sabine Gogolok, Christine Ender, Ahmed M O Elbatsh, Pär G Engström, Stefan H Stricker, Sladjana Gagrica, Ana Georgian, Ding Yu, Kin Pong U, Kevin J Harvey, Patrizia Ferretti, Patrick J Paddison, Jane E Preston, N Joan Abbott, Paul Bertone, Austin Smith, Steven M Pollard

“…We used live-cell imaging and high content image analysis tools and identified JNJ-10198409 (J101) as an agent that induces mitotic arrest at prometaphase in GNS cells but not NS cells. Antibody microarrays and kinase profiling suggested that J101 responses are triggered by suppression of the active phosphorylated form of polo-like kinase 1 (Plk1) (phospho T210), with resultant spindle defects and arrest at prometaphase. …”
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A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data. by Dobril K Ivanov, Gerrit Bostelmann, Benoit Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott-Price, Janet M Thornton

“…We utilised available microarray gene-expression data for two phenotypes (starvation-sensitive and sterile) in Drosophila. …”
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Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine. by Carina Valente, Jason Hinds, Francisco Pinto, Silvio D Brugger, Katherine Gould, Kathrin Mühlemann, Hermínia de Lencastre, Raquel Sá-Leão

“…Microarray analysis confirmed the plyNCR-RFLP results. …”
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Amogel: a multi-omics classification framework using associative graph neural networks with prior knowledge for biomarker identification by Chia Yan Tan, Huey Fang Ong, Chern Hong Lim, Mei Sze Tan, Ean Hin Ooi, KokSheik Wong

“…Abstract The advent of high-throughput sequencing technologies, such as DNA microarray and DNA sequencing, has enabled effective analysis of cancer subtypes and targeted treatment. …”
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A retrospective analysis of 6942 amniocentesis cases by Qingsha An, Yuxiao Huang, Feifei Yu, Yilun Tao, Juan Li, Xiaoze Li

“…Among the single-method cases, Chromosomal Microarray Analysis (CMA) was the most frequently selected technique (14.18%). …”
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