Whole-transcriptome analysis reveals the characteristics of intramuscular fat circRNA expression and its associated network in grazing yaks of different months of age under cold st... by Yaqian Liu, Yonggang Sun, Yincang Han, Weiqin Ding, Shengwei Jin, Jianyu Chen, Fajie Gou

“…The results may provide a reference for further investigation of the regulatory network of intramuscular fat deposition in yak.How to cite: Liu Y, Sun Y, Han Y, et al. Whole-transcriptome analysis reveals the characteristics of intramuscular fat circRNA expression and its associated network in grazing yaks of different months of age under cold stress. …”
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Unveiling the crucial role of CD8+ T cell and endothelial cell interaction in rheumatoid arthritis through the integrated analysis of spatial transcriptomics and bulk/single-cell R... by Yu Lai, Zishao Zhong, Runze Li, Tuliang Liang, Xizi He, Yuan Liu, Hao Yu, Chuanhai Zhang, Yao Xiao, Liang Liu, Hudan Pan

“…Spatial transcriptome analysis further substantiated the co-localization of CD8+ T cells and ECs. …”
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Transcriptomic characterization of human pancreatic CD206- and CD206 + macrophages by Alexander Jonsson, Olle Korsgren, Anders Hedin

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RIDDEN: Data-driven inference of receptor activity from transcriptomic data. by Szilvia Barsi, Eszter Varga, Daniel Dimitrov, Julio Saez-Rodriguez, László Hunyady, Bence Szalai

“…While several computational methods have been developed to analyze ligand-receptor interactions based on transcriptomics data, none of them focuses directly on the receptor side of these interactions. …”
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Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples by Wenyuan Yang, Hang Yu, Lian Tao, Hongjiang Xie

“…In this multidimensional regulatory study, we used transcriptome sequencing, cluster analysis, and weighted gene co-expression network analysis (WGCNA) to reveal that differentially expressed genes are enriched in multiple pathways affecting fruit acidity during apple development; malate dehydrogenase (MDH) affects the malic acid content of fruits of different varieties; and H⁺-ATPase (VHA) mainly regulates the content of vacuolar organic acids, which affects fruit acidity. …”
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The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. by Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M Thompson, Chaohan Xu, Bin Brenda Su, Huihui Fan, Javier Ordonez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne Cruz, Michael A Escamilla, Xia Li, Chun Xu

“…Transcriptome analysis revealed consistent dysfunctional processes with those determined by DMRs. …”
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Transcriptomic and metabolomic insights into flavor variations in wild and cultivated Agaricus bisporus by Zhi-Xin Cai, Zhi-Heng Zeng, Wen-Zhi Chen, Zhong-Jie Guo, Yuan-Ping Lu, Jian-Hua Liao, Hui Zeng, Mei-Yuan Chen

“…Metabolomic analysis further revealed a marked increase in uridine levels in cultivated strains (3.2-fold higher than wild-type, p < 0.01), indicating potential medicinal value, while wild strains were enriched with flavor precursors such as fumaric acid and isoleucine (fold change ≥ 2.5). …”
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STsisal: a reference-free deconvolution pipeline for spatial transcriptomics data by Yinghao Fu, Yinghao Fu, Yinghao Fu, Leqi Tian, Weiwei Zhang

“…In response to these constraints, our study introduces STsisal, a reference-free deconvolution method meticulously crafted for the intricacies of spatial transcriptomics (ST) data. STsisal leverages a novel approach that integrates marker gene selection, mixing ratio decomposition, and cell type characteristic matrix analysis to discern distinct cell types with precision and efficiency within complex tissues. …”
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Functional and transcriptomic insights into plant response to arginine-functionalized nanohydroxyapatite treatment by Chinenye L. Izuegbunam, Beate Wone, Bernard W.M. Wone

“…Additionally, R-nHA did not affect root growth in either model species but significantly promoted root and leaf growth in Triticum aestivum. Transcriptomic analysis revealed minimal transcriptional changes in Arabidopsis treated with R-nHA compared to a water control, including activated phytohormone signaling pathways and stress-responsive genes. …”
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Codes between Poles: Linking Transcriptomic Insights into the Neurobiology of Bipolar Disorder by Jon Patrick T. Garcia, Lemmuel L. Tayo

“…The development of RNA sequencing techniques has provided newer and better approaches to studying disorders at the transcriptomic level. Hence, using RNA-seq data, we employed intramodular connectivity analysis and network pharmacology assessment of disease-associated variants to elucidate the biological pathways underlying the complex nature of BPD. …”
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Differences in transcriptome characteristics and drug repositioning of Alzheimer's disease according to sex by Jingqi Shi, Minghua Zhang, Yazhuo Hu, Jing Liu, Ke Li, Xuan Sun, Siyu Chen, Jianwei Liu, Ling Ye, Jiao Fan, Jianjun Jia

“…Background: Previous studies have shown significant sex differences in AD with regarding its epidemiology, pathophysiology, clinical presentation, and treatment response. However, the transcriptome variances associated with sex in AD remain unclear. …”
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Single−cell transcriptomic landscape of sciatic nerve after transection injury by Yiben Ouyang, Mingqian Yu, Tieyuan Zhang, Haofeng Cheng, Liang Zuo, Haolin Liu, Yanjun Guan, Ao Liu, Jiajie Chen, Ruichao He, Sice Wang, Tianqi Su, Yixiao Tan, Yuhui Cu, Xiaochun Zhang, Xiaoyang Fu, Junli Wang, Jinjuan Zhao, Jiang Peng, Yu Wang

“…Vascular remodeling commenced from Day 7, while Glis progressively transitioned to mature myelinating states (Gli2/Gli5) by Day 14. …”
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Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana by Gwonjin Lee, Charlotte N. DiBiase, Beibei Liu, Tong Li, Austin G. McCoy, Martin I. Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao

“…Abstract Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. …”
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Gene expression analysis of primary graft dysfunction in adult heart transplant recipients: A cohort study by Samuel Padovani Steffen, MD, Alvaro Monteiro Perazzo, MD, MSc, Shirlyne Fabianni Dias Gaspar, MD, Ronaldo Honorato Barros Santos, MD, Domingos Dias Lourenço Filho, MD, PhD, Alexandre da Costa Pereira, MD, PhD, Luis Fernando B. da Costa Seguro, MD, PhD, Fabiana G. Marcondes-Braga, MD, PhD, Fernando Bacal, MD, PhD, Jose Eduardo Krieger, MD, PhD, Fabio Antonio Gaiotto, MD, PhD, Fabio Biscegli Jatene, MD, PhD

“…Many centers are studying PGD’s pathophysiology through epidemiological, biomarker, and transcriptome analyses. This study aims to evaluate, via transcriptomic analysis of myocardial biopsies, the gene expression profile of patients with PGD and compare it with those without PGD. …”
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Characterization of Immune Response Against <i>Mycobacterium marinum</i> Infection in Coho Salmon (<i>Oncorhynchus kisutch</i>) by Le Li, Danlei Xu, Xiaoqing Yu, Chunlei Gai, Haibin Ye, Jing Diao

“…Gene Ontology and KEGG enrichment analysis highlighted pathways such as cytokine–cytokine receptor interaction, metabolic pathways, and Toll-like receptor signaling in the kidney, while the DEGs in the liver were enriched in metabolic pathways, immune system processes, and stress and defense responses. …”
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Arginine-Mediated Liver Immune Regulation and Antioxidant Defense in Largemouth Bass (<i>Micropterus salmoides</i>): Multi-Omics Insights into Metabolic Remodeling During <i>Nocard... by Yu-Long Sun, Shuai-Liang Zhang, Feng-Feng Zhou, Yuan-Xin Qian, Yang He, Run-Zhe Zhang, Fen Dong, Qiang Chen, Han-Ying Xu, Ji-Teng Wang, Yu-Ting Deng, Tao Han

“…Moreover, the combined analysis of transcriptome and metabolome showed that <i>N. seriolae</i> infection markedly affected liver metabolism, including glutathione metabolism, arginine and proline metabolism, arachidonic acid metabolism, as well as starch and sucrose metabolism. …”
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Multi-omics exploration of chaperone-mediated immune-proteostasis crosstalk in vascular dementia and identification of diagnostic biomarkers by Wentong Li, Yiyi Zhang, Chuanhong Li, Mingyang Jiang, Dong Wang, Luomeng Chao, Luomeng Chao, Luomeng Chao, Yuxia Yang

“…Immune microenvironment analysis was conducted using CIBERSORT, while single-cell transcriptomics was analyzed within the Seurat framework.ResultsA total of 897 DEGs were identified, with functional enrichment analysis revealing significant involvement in T cell activation (p=2.84×10-3), neuroactive ligand-receptor interaction (p=6.01×10-4), and osteoclast differentiation (NES=2.83). …”
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Exploring the Causal Association Between 91 Circulating Inflammatory Proteins and Neurodegenerative Diseases: A Bidirectional Two‐Sample Mendelian Randomization and Bioinformatics... by Ziwei Gong, Rong Cao, Hong Zhu

“…RRMS patients were divided into two subgroups (C1 and C2) based on CD40 expression levels for comparative analysis. A single gene set enrichment analysis (GSEA) was conducted to investigate potential molecular mechanisms through which CD40 influences MS. …”
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Bioinformatic Analysis of C1GALT1 in Cancer: Insights Into Prognosis, Metastasis and Therapeutic Potential by Ecem Kalemoglu, Ayse Caner

“…C1GALT1, also known as core 1 β1,3‐galactosyltransferase or T‐synthase, catalyzes the formation of the core 1 O‐glycan structure and requires the chaperone Cosmc for proper folding and activity. While previous studies have implicated C1GALT1 in cancer progression, a systematic pan‐cancer analysis exploring its gene expression patterns, epigenetic regulation, immune interactions, and prognostic significance has not been fully elucidated. …”
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Disease-resistant watermelon variety against Fusarium wilt by remodeling rhizosphere soil microenvironment by Bingye Yang, Caipeng Yue, Chunhui Guo, Mingzi Zheng, Xiefeng Yao, Jinhua Xu, Sijie Huang, Mengmeng Yang

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