Epigenetic regulation of banana fruit ripening: global and specific DNA methylation profile, and characterization of DNA methylation-related genes by Dina Hermawaty, Mita Azzahra Putri, Sekar Prabhandiya, Fenny Martha Dwivany, Karlia Meitha

“…This study investigated the molecular processes behind banana ripening, focusing on DNA methylation and its role in regulating gene expression through epigenetics. Physiological changes during ripening included alterations in peel color, fruit firmness, and total soluble solids, with marked increases in starch degradation, brown spot formation, and ethylene production by day 7. …”
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COVID-19 related epigenetic changes and atopic dermatitis: An exploratory analysis by Zhenwei Tang, MD, Yu Chen, MBBS, Yuzhen Ouyang, MBBS, Yu Peng, MD, PhD, Xiaoyong Man, MD, PhD

“…In the following analysis of the causal effects of CpGs and their related gene expression, cg04543273 inhibited LMAN2 expression. …”
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A conserved fungal Knr4/Smi1 protein is crucial for maintaining cell wall stress tolerance and host plant pathogenesis. by Erika Kroll, Carlos Bayon, Jason Rudd, Victoria J Armer, Anjana Magaji-Umashankar, Ryan Ames, Martin Urban, Neil A Brown, Kim Hammond-Kosack

“…This correlation in gene expression was validated through quantitative PCR. …”
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Towards designing improved cancer immunotherapy targets with a peptide-MHC-I presentation model, HLApollo by William John Thrift, Nicolas W. Lounsbury, Quade Broadwell, Amy Heidersbach, Emily Freund, Yassan Abdolazimi, Qui T. Phung, Jieming Chen, Aude-Hélène Capietto, Ann-Jay Tong, Christopher M. Rose, Craig Blanchette, Jennie R. Lill, Benjamin Haley, Lélia Delamarre, Richard Bourgon, Kai Liu, Suchit Jhunjhunwala

“…Incorporating protein features from protein language models yields further gains and reduces the need for gene expression measurements. Guided by clinical use, we demonstrate pan-allelic generalization which effectively captures rare alleles in underrepresented ancestries.…”
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PPIH is a novel diagnostic biomarker associated with immune infiltration in cholangiocarcinoma by Jun Ye, Zhitao Chen, Chuan Zhang, Rui Xie, Haini Chen, Peng Ren

“…Methods We analyzed the expression levels, prognostic significance, and diagnostic efficiency of PPIH in CHOL using data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets, coupled with gene enrichment analyses. …”
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Harnessing the diversity of a lettuce wild relative to identify anthocyanin-related genes transcriptionally responsive to drought stress by Inés Medina-Lozano, Inés Medina-Lozano, Jérôme Grimplet, Jérôme Grimplet, Aurora Díaz, Aurora Díaz

“…These genetic variants could explain the differences in the gene expression patterns between the wild (significantly up/downregulated) and the cultivated (no significant changes) species. …”
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Exploring potential therapeutic targets for small cell lung cancer based on transcriptomics combined with Mendelian randomization analysis by Zhicheng Liao, Pengcheng Jia, Yifan Li, Zhihui Zheng, Jizhou Zhang

“…ObjectiveThe main objective of this study was to explore and identify new genetic targets in small-cell lung cancer (SCLC) through transcriptomics analysis and Mendelian randomization (MR) analysis, which will help in the subsequent development of new therapeutic interventions.MethodsIn this study, we extracted the SCLC dataset from the Gene Expression Omnibus (GEO) database, processed the data, and screened out differentially expressed genes (DEGs) using R software. …”
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Mutation-Specific Phenotypes in hiPSC-Derived Cardiomyocytes Carrying Either Myosin-Binding Protein C Or α-Tropomyosin Mutation for Hypertrophic Cardiomyopathy by Marisa Ojala, Chandra Prajapati, Risto-Pekka Pölönen, Kristiina Rajala, Mari Pekkanen-Mattila, Jyrki Rasku, Kim Larsson, Katriina Aalto-Setälä

“…Both types of HCM-CMs displayed pathological phenotype of HCM but, more importantly, we found differences between CMs carrying either MYBPC3-Gln1061X or TPM1-Asp175Asn gene mutation in their cellular size, Ca2+ handling, and electrophysiological properties, as well as their gene expression profiles. These findings suggest that even though the clinical phenotypes of the patients carrying either MYBPC3-Gln1061X or TPM1-Asp175Asn gene mutation are similar, the genetic background as well as the functional properties on the cellular level might be different, indicating that the pathophysiological mechanisms behind the two mutations would be divergent as well.…”
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Bioinformatics Analysis of Transcriptomic Data Reveals Refined Functional Networks for the Self-Renewal of Mouse Spermatogonial Stem Cells by Min Wang, Wene Zhao, Fuqiang Wang, Xiufeng Ling, Daozhen Chen, Tao Zhou, Ying Wang

“…Transcriptomics analysis could provide a comprehensive landscape of gene expression and regulation. Here, we reanalyzed a previously published transcriptome of two cell types (standing for self-renewing and differentiating SSCs correspondingly). …”
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Transcriptomics Analysis Reveals Differences in Purine and Phenylpropanoid Biosynthesis Pathways Between <i>Camellia sinensis</i> var. Shuchazao and <i>Camellia ptilophylla</i> by Waqar Khan, Peng Zheng, Binmei Sun, Shaoqun Liu

“…Shuchazao (SCZ) and <i>Camellia ptilophylla</i> (CAF)) and identified diversity in the gene expression levels and major regulatory transcription factors (TFs) for the characterization of purine alkaloids and phenylpropanoid biosynthesis pathways. …”
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hUC-MSCs Attenuate Acute Graft-Versus-Host Disease through Chi3l1 Repression of Th17 Differentiation by Weijiang Liu, Fulin Yuan, Haitao Bai, Yuanlin Liu, Xue Li, Yang Wang, Yi Zhang

“…To reveal their potential immunosuppressive molecules, we used RNA sequencing to analyze gene expression in different tissue-derived MSCs, including human bone marrow, umbilical cord, amniotic membrane, and placenta, and found that chitinase-3-like protein 1 (Chi3l1) was highly expressed in human umbilical cord mesenchymal stem cells (hUC-MSCs). …”
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Development of IgY-Based Sandwich ELISA as a Robust Tool for Rapid Detection and Discrimination of Toxigenic Vibrio cholerae by Mahdiye Bayat, Alireza Khabiri, Behzad Hemati

“…Escherichia coli BL21 (DE3) was transformed with the recombinant vectors, and gene expression was induced by IPTG. The expressed proteins were purified by affinity chromatography using Ni-NTA resins. …”
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Renewable Human Cell Model for Type 1 Diabetes Research: EndoC-βH5/HUVEC Coculture Spheroids by James M. Porter, Michael Yitayew, Maryam Tabrizian

“…Insulin secretion, metabolic activity, live cell fluorescence staining, and gene expression assays were used to compare the viability and functionality of spheroids composed of 100% beta-cells, 1 : 1 beta-cell/endothelial, and 1 : 3 beta-cell/endothelial. …”
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<i>Phyllanthus emblica</i> Prevents Adipogenesis by Regulating Histone Acetylation by Seon Kyeong Park, Yu Geon Lee, Jae-In Lee, Min-Sun Kim, Jae-Ho Park, Jin-Taek Hwang, Min-Yu Chung

“…Notably, GA effectively regulated adipogenesis-mediated gene expression through H3K9 acetylation. These findings, along with the experiment results, suggest that EFPE containing GA is a potent agent for preventing obesity by regulating H3K9 acetylation.…”
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Multiple Components of the VHL Tumor Suppressor Complex Are Frequently Affected by DNA Copy Number Loss in Pheochromocytoma by David A. Rowbotham, Katey S. S. Enfield, Victor D. Martinez, Kelsie L. Thu, Emily A. Vucic, Greg L. Stewart, Kevin L. Bennewith, Wan L. Lam

“…CNL significantly reduced gene expression and was associated with enrichment of gene targets controlled by HIF1. …”
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The Venus score for the assessment of the quality and trustworthiness of biomedical datasets by Davide Chicco, Alessandro Fabris, Giuseppe Jurman

“…We apply the Venus score to twelve datasets from multiple subdomains, including electronic health records, medical imaging, microarray and bulk RNA-seq gene expression, cheminformatics, physiologic electrogram signals, and medical text. …”
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Prevalence of asthma and related symptoms among schoolchildren in Dezful city, Southwestern Iran by Mohammad Nejadhosseini, Abdolhussein Shakurnia, Abdolkarim Sheikhi, Farhad Abolnezhadian

“…Further epidemiological studies are needed to investigate factors affecting this disease, such as indoor and outdoor environments, as well as their effects on gene expression over time.…”
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Tissue-specific effects of benzo[a]pyrene and DDT on microRNA expression profile in female rats by D. S. Ushakov, T. S. Kalinina, A. S. Dorozhkova, V. Y. Ovchinnikov, L. F. Gulyaeva

“…In part, such disorders can be mediated by the activation of nuclear receptors, resulting in the activation of protein coding gene expression and microRNAs involved in malignant transformation of cells. …”
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Liver Resection Promotes (Regulates) Proinflammatory Cytokines in Patients with Hepatocellular Carcinoma by Farshid Fathi, Behnam Sanei, Mazdak Ganjalikhani Hakemi, Reza F. Saidi, Abbas Rezaei

“…After 60 and 90 minutes of LR, IL-6 gene expression was significantly increased P<0.001−0.05. …”
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Autism-Like Behavior and Epigenetic Changes Associated with Autism as Consequences of In Utero Exposure to Environmental Pollutants in a Mouse Model by Denise S. Hill, Robert Cabrera, Deeann Wallis Schultz, Huiping Zhu, Wei Lu, Richard H. Finnell, Bogdan J. Wlodarczyk

“…Brain samples from Mn, Pb, and VPA treated and control animals were evaluated for changes in CpG island methylation in promoter regions and associated changes in gene expression. The Chd7 gene, essential for neural crest cell migration and patterning, was found to be hypomethylated in each experimental animal tested compared to water-treated controls. …”
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