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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Molecular profiles of tumor contrast enhancement: A radiogenomic analysis in anaplastic gliomas by Xing Liu, Yiming Li, Zhiyan Sun, Shaowu Li, Kai Wang, Xing Fan, Yuqing Liu, Lei Wang, Yinyan Wang, Tao Jiang

“…Gene set enrichment analysis (GSEA), significant analysis of microarray, generalized linear models, and Least absolute shrinkage and selection operator algorithm were used to explore radiogenomic and prognostic signatures of AG patients. …”
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Identifying a unique chromosomal pattern to predict the gemcitabine response in patients with cholangiocarcinoma by Sutheemon Techa-ay, Sasithorn Watcharadetwittaya, Raksawan Deenonpoe, Prakasit Sa-ngiamwibool, Chanita Panwoon, Watcharin Loilome, Poramate Klanrit, Anchalee Techasen, Yaovalux Chamgramol, Manida Suksawat, Napat Armartmuntree, Thomas O’Connor, Hideyuki Saya, Malinee Thanee

“…This signature pattern could provide the knowledge to improve a predictive biomarker for GEM response, benefitting for individual CCA patient management and chemotherapeutic selection.…”
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A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. by Katherine James, Shereen Al-Ali, Jessica Tarn, Simon J Cockell, Colin S Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin T Pease, Paul Emery, Peter Lanyon, John A Hunter, Monica Gupta, Michele Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, UK Primary Sjögren’s Syndrome registry, Anil Wipat, Julia Newton, David E Jones, John Isaacs, Jennifer Hallinan, Wan-Fai Ng

“…Finally, gene set enrichment analysis (GSEA) was used as a feature selection technique for input into a support vector machine (SVM) classifier. …”
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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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Immune-related gene characterization and biological mechanisms in major depressive disorder revealed based on transcriptomics and network pharmacology by Shasha Wu, Shasha Wu, Qing Jiang, Jinhui Wang, Jinhui Wang, Daming Wu, Yan Ren

“…Subsequently, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cytoscape plugin CluGO, and Gene Set Enrichment Analysis (GSEA) were utilized to identify immune-related genes. The final selection of immune-related hub genes was determined through the least absolute shrinkage and selection operator (Lasso) regression analysis and PPI analysis. …”
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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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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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