Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins by E. A. Antropova, T. M. Khlebodarova, P. S. Demenkov, A. S. Venzel, N. V. Ivanisenko, A.  D.  Gavrilenko, T.  V. Ivanisenko, A. V. Adamovskaya, P. M. Revva, I. N. Lavrik, V. A. Ivanisenko

“…The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. …”
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Cuproptosis-Related Signature Predicts the Prognosis, Tumor Microenvironment, and Drug Sensitivity of Hepatocellular Carcinoma by Xiangjun Qi, Jiayun Guo, Guoming Chen, Caishan Fang, Leihao Hu, Jing Li, Chi Zhang

“…Molecular characterization analysis of CRGs, including differential gene expression analysis, mutation analysis, copy number variation (CNV) analysis, Kaplan-Meier analysis, and immune regulator prioritization analysis, was implemented. …”
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Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH by Tobias Obermann, Teri Sakshaug, Vishnu Vignesh Kanagaraj, Andreas Abentung, Mirta Mittelstedt Leal de Sousa, Lars Hagen, Antonio Sarno, Magnar Bjørås, Katja Scheffler

“…Interestingly, no association was found between genomic OG deposition and gene expression changes upon loss of OGG1 and MUTYH. Regardless of DNA glycosylase activity, OG in promoter regions correlated with expression of genes related to metabolic processes and damage response pathways indicating that OG functions as a cellular stress sensor to regulate transcription. …”
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Effects of the Highly COX-2-Selective Analgesic NSAID Etoricoxib on Human Periodontal Ligament Fibroblasts during Compressive Orthodontic Mechanical Strain by Christian Kirschneck, Erika Calvano Küchler, Michael Wolf, Gerrit Spanier, Peter Proff, Agnes Schröder

“…Etoricoxib at 3.29 μM and 5.49 μM significantly inhibited PG-E2 synthesis, but not COX-2 and IL-6 gene expression nor RANK-L-/OPG-mediated osteoclastogenesis or angiogenesis (VEGF-A). …”
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FBR2 modulates ferroptosis via the SIRT3/p53 pathway to ameliorate pulmonary fibrosis by Yu Cheng, Yang Jiao, Wan Wei, Mengjia Kou, Yaodong Cai, Yang Li, Hao Li, Tonghua Liu

“…Assessments encompassed histopathology, ELISA for cytokine detection, IHC and Western blot for protein expression analysis, and qRT-PCR for gene expression quantification. Transmission electron microscopy (TEM) was used to observe mitochondrial morphology. …”
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Lactoferrin Modulates Radiation Response Under Hypoxic Conditions, Possibly Through the Regulation of ROS Production in a Cell Type-Specific Manner by Daitoku Murakami, Takahiro Fukazawa, Michihito Kyo, Mutsumi Miyauchi, Shigehiro Ono, Tomonao Aikawa, Nobuyuki Hirohashi, Keiji Tanimoto

“…RNA-seq and gene set enrichment analysis showed that LF treatment regulated gene expression related to the cell cycle, apoptosis, inflammation, and the NRF2 antioxidant signaling pathway. …”
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Amygdalin Promotes Fracture Healing through TGF-β/Smad Signaling in Mesenchymal Stem Cells by Jun Ying, Qinwen Ge, Songfeng Hu, Cheng Luo, Fengyi Lu, Yikang Yu, Taotao Xu, Shuaijie Lv, Lei Zhang, Jie Shen, Di Chen, Peijian Tong, Luwei Xiao, Ju Li, Hongting Jin, Pinger Wang

“…Fracture calluses were then harvested and subjected to radiographic, histological, and biomechanical testing, as well as angiography and gene expression analyses to evaluate fracture healing. …”
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Toward autism spectrum disorders and Williams-Beuren syndrome co-occurrence condition in Tunisian patients: Genetic insights by Rim Khelifi, Afef Jelloul, Houda Ajmi, Wafa Slimani, Sarra Dimassi, Khouloud Rjiba, Manel Dardour, Moez Gribaa, Ali Saad, Soumaya Mougou-Zerelli

“…Furthermore, our findings highlight the potential role of genetic factors and regulatory elements within the deleted region in modulating gene expression, notably the HIP1 gene. This underscores the implications of gene dosage and environmental factors in the broader WBS region, notably with language and social development.ConclusionThe presence of ASD in WBS patients emphasizes the need to investigate all WBS patients for autistic traits to establish a better genotype–phenotype correlation. …”
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Integrative Bioinformatics Analysis to Identify Key Ferroptosis-Related Genes and Immune Infiltration in Aortic Aneurysm and Dissection: Implication of PTGS2 by An W, Luo J, Zhang C, Xiao Q

“…However, ferroptosis-related genes (FRGs) have not been systematically identified and verified in AAD.Methods and Results: Seven human AAD datasets downloaded from Gene Expression Omnibus were analyzed, and 113 potential AAD-related FRGs were identified. …”
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A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential by M. P. Ponomarenko, I. V. Chadaeva, P. M. Ponomarenko, A. G. Bogomolov, D. Yu. Oshchepkov, E. B. Sharypova, V. V. Suslov, A. V. Osadchuk, L. V. Osadchuk, Yu. G. Matushkin

“…Belyaev’s discovery of destabilizing selection during the domestication of animals and that this selection affects only gene expression regulation (not gene structure) and influences systems of neuroendocrine control of ontogenesis in a stressful environment. …”
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Expression and prognostic significance of the m6A RNA methylation regulator HNRNPC in HNSCC by Yulin Zhang, Yixu Wang, Jilin Peng, Kun Zhao, Ling Li, Yuan Zhang, Ziyu Zhai, Sijie Yuan, Shichao Li, Shichao Li, Shichao Li, Fanglei Ye, Le Wang

“…Further experiments were performed in patient samples, stable cell lines, and a murine xenograft tumor model.ResultsA reliable survival risk model of m6A was constructed based on the TCGA database. Gene Expression Omnibus (GEO), normal and tumor tissue microarrays (TMA), and tumor tissue samples from patients with HNSCC were observed that a high level of HNRNPC expression was closely linked to a poor prognosis among patients. …”
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Serum levels of oxidative stress, IL-8, and pepsinogen I/II ratio in Helicobacter pylori and gastric cancer patients: potential diagnostic biomarkers by Marwa Nasier-Hussain, Jaleel Najah Samanje, Khatere Mokhtari, Mohsen Nabi-Afjadi, Zeinab Fathi, Asieh Hoseini, Elham Bahreini

“…The findings were substantiated using various data analysis platforms such as Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN (The University of ALabama at Birmingham CANcer data analysis), cBioPortal, and TIMER (Tumor IMmune Estimation Resource). …”
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Fade into you: genetic control of pigmentation patterns in red-flesh apple (Malus domestica) by Pierre Bouillon, Pierre Bouillon, Etienne Belin, Anne-Laure Fanciullino, Sandrine Balzergue, Sandrine Balzergue, Sylvain Hanteville, Yao Letekoma, Maryline Cournol, Fatima Faris, Andréa Bouanich, Dimitri Bréard, Frédéric Bernard, Jean-Marc Celton

“…Expression of MdGSTU22 was linked to a differentially methylated region (DMR) suggesting a potential environmental effect on the epigenetic control of gene expression involved in color fading. Altogether, these results provide the first characterization and functional identification of color fading in apple fruit flesh.…”
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Deciphering Immunometabolic Landscape in Rheumatoid Arthritis: Integrative Multiomics, Explainable Machine Learning and Experimental Validation by Dong Q, Wu J, Zhang H, Chen X, Xu X, Chen J, Shi C, Luo L, Zhang D

“…We further analyzed single-cell and bulk transcriptomes to investigate differential gene expression, immune cell interactions, and relevant biological processes. …”
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Implication of fibroblast growth factor 7 in ovarian cancer metastases and patient survival by Laura F. Mortan, Laura F. Mortan, Brooke A. Meelheim, Justin Garland, Justin Garland, Jacqueline A. Bohn, Zitha Redempta Isingizwe, Doris M. Benbrook, Doris M. Benbrook

“…Significances of differential gene expression and patient prognosis were determined by volcano plot and log-rank test, respectively.ResultsTumor transcriptomes exhibited higher endothelial cells, oxygenation, proteasome activity, and metabolism in comparison to ascites, but similar percentages of cancer-associated fibroblasts and immune cells. …”
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Integrating transcriptomics, metabolomics, and network pharmacology to investigate multi-target effects of sporoderm-broken spores of Ganoderma lucidum on improving HFD-induced dia... by Lidan Hu, Lili Yu, Zhongkai Cao, Yue Wang, Caifeng Zhu, Yayu Li, Jiazhen Yin, Zhichao Ma, Xuelin He, Ying Zhang, Wunan Huang, Yuelin Guan, Yue Chen, Xue Li, Xiangjun Chen

“…GLP significantly suppressed the inflammations by impacting glucose and energy metabolism-related gene expression (Igfbp1 and Angptl4) and enhanced metabolic biomarkers of 4-Aminocatechol. …”
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Exosome-mediated delivery of miR-9 induces cancer-associated fibroblast-like properties in human breast fibroblasts by Sara Baroni, S Romero-Cordoba, I Plantamura, M Dugo, E D’Ippolito, A Cataldo, G Cosentino, V Angeloni, A Rossini, M G Daidone, M V Iorio

“…Consistently with the biological effects observed, gene expression profiles of NFs upon transient transfection with miR-9 show the modulation of genes mainly involved in cell motility and extracellular matrix remodeling pathways. …”
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Comprehensive analysis of the expression and prognostic value of ARMCs in pancreatic adenocarcinoma by Guanxiang Zhuo, Shengzhai Lin, Fei Yuan, Qiaoling Zheng, Yinpin Guo, Zuwei Wang, Jianfei Hu, Meihong Yao, Fuxiu Zhong, Shi Chen, Yanling Chen, Huixing Chen

“…Methods We used the The Cancer Genome Atlas (TCGA) database for survival analysis. Then, Gene Expression Profiling Interactive Analysis (GEPIA), the cBioPortal database, the Human Protein Atlas (HPA), Kaplan-Meier Plotter, LinkedOmics Database, Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG), Cytoscape and Timer were used to analyze the relationship between ARMCs and PAAD. …”
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High-altitude hypoxia aggravated neurological deficits in mice induced by traumatic brain injury via BACH1 mediating astrocytic ferroptosis by Peng Zou, Tianjing Li, Zixuan Cao, Erwan Yang, Mingdong Bao, Haofuzi Zhang, Zhuoyuan Zhang, Dan Liu, Min Zhang, Xiangyu Gao, Junmiao Ge, Xiaofan Jiang, Zhicheng Tian, Peng Luo

“…Single-nuclear RNA sequencing was subsequently employed to further reveal differential gene expression profiles in high-altitude TBI. We found a significant increase in ferroptosis of astrocytes in cases of high-altitude TBI compared to those at low-altitude TBI. …”
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Spironolactone Protects against Diabetic Cardiomyopathy in Streptozotocin-Induced Diabetic Rats by Wenjuan Liu, Wei Gong, Min He, Yemei Liu, Yeping Yang, Meng Wang, Meng Wu, Shizhe Guo, Yifei Yu, Xuanchun Wang, Fei Sun, Yiming Li, Linuo Zhou, Shengmei Qin, Zhaoyun Zhang

“…Cardiac structure was investigated with transmission electron microscopy and pathological examination; immunohistochemistry was performed to detect nitrotyrosine, collagen-1, TGF-β1, TNF-α, and F4/80 expression; and gene expression of markers for oxidative stress, inflammation, fibrosis, and energy metabolism was detected. …”
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