In silico analysis of the oncogenic role of myoferlin (MYOF) and suggestion of folate as a potential therapeutic for brain cancer in the Caucasian population by Saanvi Muthuchetty

“…Methods In the current study, the expression, pathways, mutations, and interacting genes of MYOF were analyzed via bioinformatics analysis, which included computational drug discovery and spatial transcriptomics coupled with generative artificial intelligence experiments that were performed to elucidate the role of folate in MYOF knockdown. …”
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The multi-omics analysis identifies a novel endoplasmic reticulum stress and immune related genes signature in lung adenocarcinoma by Danhe Huang, Yuying Liu, Mingyu Yuan, Xiongwei Wang, Lianqing Hong

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Genome-Wide Identification and Expression Analysis of <i>UBP</i> Genes in Peppers (<i>Capsicum annuum</i> L.) by Xuerui Chang, Tiantian Wang, Jiaxin Huang, Jia Xu, Yangyang Ruan, Yanping Liang, Jing Wang

“…Subcellular localization studies indicated that all <i>CaUBPs</i> are localized in the nucleus. Phylogenetic analysis categorized the 40 CaUBPs into 11 distinct subfamilies (G1–G11), with the largest subfamily comprising seven members. …”
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RNA-seq analysis identifies key genes and signaling pathways involved in androgen promotion of sebaceous gland proliferation in Hetian sheep by Zhiya Feng, Zhigang Li, Wanwan Peng, Jianping Zhang, Chunyang Li, Ruijun Shi, Shuwei Li

“…This study investigated how androgens influence SGs hyperplasia in sheep by combining morphological assessments with transcriptomic analysis. Histological examination revealed a significant increase (P < 0.05) in both the number and average size of SGs in the testosterone-treated groups across four concentration gradients compared to the control group. …”
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Identification of biomarkers associated with energy metabolism in hypertrophic cardiomyopathy and exploration of potential mechanisms of roles by Songyan Cai, Tianying Jin, Mintong Liu, Qingyuan Dai

“…Here, biomarkers related to energy metabolism in HCM were identified through bioinformatics analysis.MethodsHCM transcriptome data were acquired from the GEO (GSE36961) database for comparative analysis in order to identify differentially expressed genes (DEGs). …”
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Genome-wide study and expression analysis of soybean ERF transcription factors and overexpression of GmERF205 enhances drought resistance in soybean by Nan Wu, Yongqi Feng, Tao Jiang, Zhaobo Li, Yulan Liu, Minghao Yuan

“…In both transcriptome data and fluorescence quantitative analysis, the GmERF205 gene was significantly upregulated. …”
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Deciphering human endogenous retrovirus expression in colorectal cancers: exploratory analysis regarding prognostic value in liver metastasesResearch in context by Julien Viot, Romain Loyon, Nawfel Adib, Pierre Laurent-Puig, Aurélien de Reyniès, Fabrice André, Franck Monnien, Thierry André, Magali Svrcek, Anthony Turpin, Zohair Selmani, Laurent Arnould, Laura Guyard, Nicolas Gilbert, Anthony Boureux, Olivier Adotevi, Angélique Vienot, Syrine Abdeljaoued, Dewi Vernerey, Christophe Borg, Daniel Gautheret

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Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes by Víctor Chano, Renata Callegari Ferrari, Tania Domínguez-Flores, Karuna Shrestha, Barbara Fussi, Hannes Seidel, Oliver Gailing, Katharina B. Budde

“…The analysis yielded 395 and 500 Differentially Expressed Genes (DEGs) along the response for ADB-tolerant FAR3 and FS36, respectively, while ADB-susceptible UW1 and UW2 revealed 194 and 571 DEGs, respectively, with most DEGs found exclusively in just one of the genotypes. …”
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Preliminary Analysis of the Salt-Tolerance Mechanisms of Different Varieties of Dandelion (<i>Taraxacum mongolicum</i> Hand.-Mazz.) Under Salt Stress by Wei Feng, Ran Meng, Yue Chen, Zhaojia Li, Xuelin Lu, Xiuping Wang, Zhe Wu

“…Our results showed that 222 significantly altered metabolites mainly enriched in arginine biosynthesis and pyruvate metabolism according to a KEGG database analysis in variety A, while 147 differential metabolites were predominantly enriched in galactose metabolism and the pentose phosphate pathway in variety B. …”
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Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. by Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M Monk, Rayees Rahman, Mini Kamboj, Bernhard O Palsson, Weigang Qiu, Joao B Xavier

“…A detailed analysis of one patient's timeline shows how this mutation can emerge in vivo and drive rapid evolution of resistance while the patient received cancer treatment, a bone marrow transplantation, and antibiotics up to the point of causing the patient's death. …”
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Immunogenic cell death-related genes as prognostic biomarkers and therapeutic insights in uterine corpus endometrial carcinoma: an integrative bioinformatics analysis by Tianfei Yi, Zhenglun Yang, Peng Shen, Yan Huang

“…IntroductionImmunogenic cell death (ICD) is the phenomenon in which tumor cells undergo the transition from a non-immunogenic state to an immunogenic state upon their demise as a result of external stimuli. While ICD systems have been widely adopted in oncological research, their specific utilization for Uterine Corpus Endometrial Carcinoma (UCEC) investigations has received comparatively little attention.MethodsThe ICD score was assessed using single-sample gene set enrichment analysis (ssGSEA). …”
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Comparative Analysis of the Biochemical and Molecular Responses of <i>Nannochloropsis gaditana</i> to Nitrogen and Phosphorus Limitation: Phosphorus Limitation Enhances Carotenogen... by Sun Young Kim, Hanbi Moon, Yong Min Kwon, Kyung Woo Kim, Jaoon Young Hwan Kim

“…These results were generally consistent with the gene expression pattern observed in transcriptomic analysis. This integrated analysis shows that phosphorus limitation can be an economically competitive solution by enhancing valuable carotenoids while maintaining lipid and biomass production in <i>N. gaditana</i>.…”
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Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury by Fan Lu, Ting Huang, Ruichang Chen, Haiyan Yin

“…In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. …”
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Analysis of immune status and prognostic model incorporating lactate metabolism and immune-related genes in clear cell renal cell carcinoma by Jun Wu, Yuqian Wu, Yefeng Sun, Jianhang You, Wenjie Zhang, Tao Zhao

“…Immune microenvironment analysis demonstrated that the high‐risk group exhibited higher immune cell infiltration, while the low‐risk group was enriched for metabolism‐related pathways. …”
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Cardiovascular diseases in the elderly: possibilities for modulating autophagy using non-coding RNAs by Silvia Scalabrin, Stefano Cagnin, Stefano Cagnin

“…Finally, we conducted a comprehensive meta-analysis of transcriptomic data to underscore the paramount importance of autophagy while demonstrating it as a process that is frequently dysregulated in both cardiac and vascular cells under pathological conditions. …”
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Analysis of Alternative Splicing Events and Identification of Key Genes in <i>Brassica napus</i> Leaves Infected by <i>Leptosphaeria biglobosa</i> by Xinning Ma, Lin Yuan, Jiuru Huangfu, Mengjiao Yan, Chen Guo, Lili Zhao, Hongxia Sun, Xiaoqing Jia, Ziqin Li, Haiyan Huangfu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to elucidate the biological functions of differentially spliced genes at various time points, while Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify key modules and hub genes. …”
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A prognostic PET radiomic model for risk stratification in non-small cell lung cancer: integrating radiogenomics and clinical features to predict survival and uncover tumor biology... by Parisa Taheri, Aaron Golden

“…Integration of clinical features and the radiomic risk score in a nomogram demonstrated enhanced efficacy, achieving AUCs greater than 0.85. Radiogenomic analysis revealed that while the low-risk group indicated anti-tumor immunity, the high-risk group exhibited transcriptomic characteristics associated with enhanced tumor aggressiveness, with consistent correlations between risk group membership, oncogenic pathways, immune cell types, and critical gene alterations. …”
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Integrative analysis of epigenetic subtypes in acute myeloid Leukemia: A multi-center study combining machine learning for prognostic and therapeutic insights. by Jincan Li, Shengyue Wang

“…Immune microenvironment analysis employed multiple deconvolution methods (ESTIMATE, CIBERSORT, xCell) and pathway analysis (GSVA, GSEA). …”
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Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrum L.) Varieties by Choy Yuen Khew, Jennifer Ann Harikrishna, Wei Yee Wee, Ee Tiing Lau, Siaw San Hwang

“…Gene Ontology (GO) enrichment analysis further supports functions of DEGs between flower and fruit in the categories of carbohydrate metabolic processes, embryo development, and DNA metabolic processes while the DEGs in fruit relate to biosynthetic process, secondary metabolic process, and catabolic process. …”
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Investigation of transcriptional and immunological disparities among patient groups with varied prognostic risk factors in cholangiocarcinoma by Baoluhe Zhang, Bao Jin, Xiang'an Wu, Jiali Xing, Xiao Liu, Xueshuai Wan, Haifeng Xu, Yiyao Xu, Yilei Mao, Qian Chen, Yating Bai, Mei Guan, Shunda Du

“…Among the 70 patients, the TP53 gene mutation frequency was the highest (53%), while FLG gene mutation occurred exclusively in the long PFS group. …”
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