Prognostic analysis of bladder cancer with neddylation-related genes by Huang Xiaolong, Deng Min, Zhang Sizhou, Hu Daorong, Pan Juncheng, Wang Yanjian, Li Jie Gu Hong, Zheng Ji, Wu Qingjian

“…LASSO and Cox regression analyses subsequently identified six key genes: CUL1, PUM2, UBE2D3, HIF3A, COPS2, and DDB1. Transcriptomic data and RT-qPCR findings indicated that PUM2 and HIF3A exhibited high expression levels in normal tissues, while DDB1 showed increased expression in tumor tissues; no significant changes were observed for CUL1, COPS2, and UBE2D3. …”
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Computational analysis of DEHP’s oncogenic role in colorectal cancer by Zhou Zhu, Jian Qin, Chungang He, Shuangyou Wang, Yaolin Lu, Shuai Wang, Xiaogang Zhong

“…The PPI network highlighted 14 candidate genes, with machine learning methods narrowing down to three key genes: CDK1, CDK4, and BCL2. SHAP analysis showed CDK1 and CDK4 as top contributors, while ssGSEA revealed significant correlations between these genes and immune cell infiltration. …”
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Neuroprotective effects of ethanol extraction from Rubia yunnanensis Diels on chronic cerebral hypoperfusion: modulation of the System Xc-/GSH/GPX4 axis to alleviate oxidative stre... by Jianghao Cheng, Xiaoxia Ma, Jie Tao, Xiaoli Jiang, Pu Chen, Xiaohua Duan

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Transcriptional regulatory network analysis of microglia in multiple sclerosis by CAI Qiangwei, SUN Feng, WU Wenyu, SHAO Fuming, GAO Zhengliang, JIN Shengkai

“…The results of GO and KEGG pathway analysis showed that in gray matter microglia, functions such as endocytosis, ion homeostasis, and lipid localization were downregulated during disease progression, while in white matter microglia, functions such as protein folding, cytoplasmic translation, and response to thermal stimuli were upregulated. …”
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Comprehensive characterization of NK cell-related genes in cutaneous melanoma identified a novel prognostic signature for predicting the prognosis, immunotherapy, and chemotherapy... by Haili Ma, Jian Liu, Huan Jin, Min Zhang, Qian Liang, Zhiqiang Guo

“…Single-cell transcriptomes from CM were analyzed in conjunction with immune genes to identify NKIGs. …”
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Transcriptional analysis of Camellia Huana under low-phosphorus stress by Fan Wu, Lang Xia, Xin Xie, Yue Zhang, Biyin Pan

“…Abstract The molecular mechanism underlying the response of C. huana to low-phosphorus (P) stress was explored with transcriptome sequencing to analyze the genome-wide responses of plants exposed to different durations of low-P stress. …”
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Molecular Mechanism During Mycelium Subculture Degeneration of <i>Volvariella volvacea</i> by Lidan Feng, Lujuan Wang, Yuanxi Lei, Jie Li, Fengyun Zhao

“…Thus, five generations of subcultured strains (M1–M5) were obtained after 20 months of mycelial subculturing, their production traits were determined, and transcriptomic analysis was performed using RNA-seq; the differentially expressed genes were verified via RT-qPCR. …”
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Pulsed Electric Field Treatment Modulates Gene Expression and Stress Responses in Fusarium-Infected Malting Barley by Pavel Svoboda, Jaroslava Ovesná, Štěpán Helmer, Milena Stránská

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Investigation of the therapeutic effects and mechanisms of Houpo Mahuang Decoction on a mouse model of chronic obstructive pulmonary disease by Shanlan Li, Ziqi Dai, Tong Zhang, Zhuoqian Guo, Feng Gao, Xuehao Cheng, Jin An, Yixuan Lin, Xiaomin Xiong, Nan Wang, Guanghui Jiang, Bing Xu, Haimin Lei

“…Network pharmacology and transcriptomics further revealed the mechanism, indicating that the IL-17 signaling pathway might been instrumental in the inhibitory effect of HPMHD on mouse model of COPD. …”
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Integrative multi-omics analysis to gain new insights into COVID-19 by Setegn Eshetie, Karmel W. Choi, Elina Hyppönen, Beben Benyamin, S. Hong Lee

“…In the omics-exposome model, where individual omics layers were simultaneously fitted with exposome data, the contributions of genome and metabolome were diminished and considered negligible, whereas the effects of the transcriptome showed minimal change. Through mediation analysis, the findings revealed that exposomic factors mediated about 60% of the genome and metabolome’s effects, while having a relatively minor impact on the transcriptome, mediating only 7% of its effects. …”
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Interpretable and integrative analysis of single-cell multiomics with scMKL by Samuel D. Kupp, Ian A. VanGordon, Mehmet Gönen, Sadık Esener, Sebnem Ece Eksi, Çiğdem Ak

“…It outperforms existing methods while delivering interpretable results that identify key transcriptomic and epigenetic features, as well as multimodal pathways– that existing methods have failed to achieve, in breast, lymphatic, prostate, and lung cancers. …”
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Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis by Alejandro Jiménez-González, Sebastian Cristian Treitli, Priscila Peña-Diaz, Anna Janovská, Vladimír Beneš, Petr Žáček, Vladimír Hampl

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Molecular and spatial analysis of tertiary lymphoid structures in Sjogren’s syndrome by Saba Nayar, Jason D. Turner, Saba Asam, Eanna Fennell, Matthew Pugh, Serena Colafrancesco, Onorina Berardicurti, Charlotte G. Smith, Joe Flint, Ana Teodosio, Valentina Iannizzotto, David H. Gardner, Joel van Roon, Ilya Korsunsky, Dawn Howdle, Roche Fibroblast Network Consortium, Andreas P. Frei, Kara G. Lassen, Simon J. Bowman, Wan-Fai Ng, Adam P. Croft, Andrew Filer, Benjamin A. Fisher, Christopher D. Buckley, Francesca Barone

“…Abstract Tertiary lymphoid structures play important roles in autoimmune and non-autoimmune conditions. While many of the molecular mechanisms involved in tertiary lymphoid structure formation have been identified, the cellular sources and temporal and spatial relationship remain unknown. …”
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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

“…Methods: We combined Mendelian randomization and transcriptome analysis for data-driven explorations. …”
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Deciphering the prognostic significance of WDR77 in gliomas: a comprehensive analysis by Hanwen Lu, Bingchang Zhang, Wenhua Li, Zhanxiang Wang

“…Transcriptome data was obtained from CGGA (mRNAseq-693, mRNAseq-325) and TCGA databases for analysis. …”
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Phylogenetic and expression analysis of terpenoid synthase gene family in Eustoma grandiflorum by LI Xinyuan, LIANG Yuwei, FANG Huiyi, SUN Fuhui, ZHANG Liangsheng

“…Transcriptome expression analysis showed that only EgTPS-g1, EgTPS-g2, and EgTPS-g3 were expressed in the early stages of petal development, and TPS-a and TPS-b subfamily members were not expressed in the petals of E. grandiflorum, likely contributing to the lack of floral fragrance. …”
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Multiomic analysis of monocyte-derived alveolar macrophages in idiopathic pulmonary fibrosis by Miaomiao Zhang, Jinghao Zhang, Haisheng Hu, Yuan Zhou, ZhiWei Lin, Hui Jing, Baoqing Sun

“…Abstract Background Monocyte-derived alveolar macrophages (Mo_AMs) are increasingly recognised as potential pathogenic factors for idiopathic pulmonary fibrosis (IPF). While scRNAseq analysis has proven valuable in the transcriptome profiling of Mo_AMs, the integration analysis of multi-omics may provide additional dimensions of understanding of these cellular populations. …”
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Spatiotemporal dynamic changes of meningeal microenvironment influence meningeal lymphatic function following subarachnoid hemorrhage: from inflammatory response to tissue remodeli... by Bingrui Zhu, Changming Liu, Ming Luo, Jiarui Chen, Sixuan Tian, Tiantong Zhan, Yibo Liu, Haocheng Zhang, Zhen Wang, Jianmin Zhang, Yuanjian Fang, Sheng Chen, Xiaoyu Wang

“…Methods We employed bioinformatics analysis of single-cell RNA sequencing and spatial transcriptomics to characterize the spatiotemporal dynamic changes in the early meningeal microenvironment post-SAH. …”
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Exosomes originating from neural stem cells undergoing necroptosis participate in cellular communication by inducing TSC2 upregulation of recipient cells following spinal cord inju... by Shiming Li, Jianfeng Li, Guoliang Chen, Tao Lin, Penghui Zhang, Kuileung Tong, Ningning Chen, Shaoyu Liu

“…We previously demonstrated that inhibiting neural stem cells necroptosis enhances functional recovery after spinal cord injury. While exosomes are recognized as playing a pivotal role in neural stem cells exocrine function, their precise function in spinal cord injury remains unclear. …”
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Spatiotemporal analysis of lung immune dynamics in lethal Coccidioides posadasii infection by Oscar A. Davalos, Aimy Sebastian, Nicole F. Leon, Margarita V. Rangel, Nadia Miranda, Deepa K. Murugesh, Ashlee M. Phillips, Katrina K. Hoyer, Nicholas R. Hum, Gabriela G. Loots, Dina R. Weilhammer

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