Machine learning integration of single-cell and bulk transcriptomics identifies fibroblast-driven prognostic markers in colorectal cancer by Ning Zhang, Ruiyan Liu, Siya Wu, Chenxi Feng, Boxiang Wang, Qiaoqiao Zheng, Linru Jie, Ruihua Kang, Xiaoli Guo, Xiaoyang Wang, Shaokai Zhang, Jiangong Zhang

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Transcriptomic and metabolomic insights into temperature-dependent changes in catechin and anthocyanin accumulation in tea plants with different leaf colors by Jingbo Yu, Qianying Wang, Wenli Wang, Ruihong Ma, Changqing Ding, Kang Wei, Liyuan Wang, Shibe Ge, Yuanzhi Shi, Xin Li

“…Low temperatures enhanced the expression of ANTHOCYANIDIN SYNTHASE (ANS) in ZJ while inhibiting the expression of ANTHOCYANIDIN REDUCTASE (ANR) and LEUCOANTHOCYANIDIN REDUCTASE (LAR). …”
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MOGAN for LUAD Subtype Classification by Integrating Three Omics Data Types by Haibin He, Longxing Wang, Mingyue Ma

“…Results Two subtypes, MOGANTPM_S1 and MOGANTPM_S2, were identified using immune cell infiltration analysis and the integrated multi‐omics data. MOGANTPM_S1 patients displayed higher immune cell infiltration, better prognosis, and sensitivity to immune checkpoint inhibitors (ICIs), while MOGANTPM_S2 had lower immune cell infiltration, poorer prognosis, and were insensitive to ICIs. …”
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GePIF4 Increases the Multi-Flower/Capsule-Bearing Traits and Gastrodin Biosynthesis in <i>Gastrodia elata</i> by Yue Xu, Zhiqing Wu, Yugang Gao, Pu Zang, Xinyu Yang, Yan Zhao, Qun Liu

“…The natural materials were selected by multi-capsule and few-capsule for transcriptome analysis to screen the differentially expressed genes (DEGs); the candidate gene <i>GePIF4</i> was suspected to regulate the formation of multiple flowers and fruits. …”
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Toxic Effects of Acute Water Selenium Exposure on <i>Litopenaeus vannamei</i>: Survival, Physiological Responses, Transcriptome, and Intestinal Microbiota by Xinghui Luo, Jian Chen, Asare Derrick, Gongyu Li, Hongming Wang, Zhihao Xue, Lili Shi, Shuang Zhang

“…However, MDA levels showed no significant intergroup differences (<i>p</i> > 0.05). Hemocyte transcriptomic analysis revealed 2103 differentially expressed genes (DEGs) (1294 upregulated, 809 downregulated) in the S2 group compared to CON. …”
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Adaptation responses to salt stress in the gut of Poecilia reticulata by Hyerim Lee, Hyunjae Yeo, Jihye Park, Keunsoo Kang, Sun-Ju Yi, Kyunghwan Kim

“…Transcriptomic analysis identified key genes involved in osmoregulation, tissue remodeling, and immune modulation. …”
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The pseudo-type response regulator gene Clsc regulates rind stripe coloration in watermelon by Dongming Liu, Jinfang Liang, Quanquan Liu, Yaxin Chen, Shixiang Duan, Dongling Sun, Huayu Zhu, Junling Dou, Huanhuan Niu, Sen Yang, Shouru Sun, Jianbin Hu, Luming Yang

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Sperm-borne mRNAs: potential roles in zygote genome activation and epigenetic inheritance by Betina González, Candela Rocío González

“…Here, we curated mouse transcriptomic data from mature sperm and selected the most abundant mRNAs (above the 0.7 quantile). …”
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Unraveling the genetic architecture of blueberry fruit quality traits: major loci control organic acid content while more complex genetic mechanisms control texture and sugar conte... by Heeduk Oh, Molla F. Mengist, Guoying Ma, Lara Giongo, Marti Pottorff, Jessica A. Spencer, Penelope Perkins-Veazie, Massimo Iorizzo

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Long-term thermal acclimation enhances heat resistance of Hong Kong catfish (Clarias fuscus) by modulating gill tissue structure, antioxidant capacity and immune metabolic pathways by Cunyu Duan, Dayan Zhou, Ruiqing Feng, Xiaolong Li, Lei Yang, Xinyi Li, Guangli Li, Huapu Chen, Yu Liao, Changxu Tian

“…Transcriptome analysis identified 520 and 463 differentially expressed genes in the NT and HT groups, respectively, in response to acute temperature changes. …”
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Transcriptome Profiling Reveals Genetic Basis of Muscle Development and Meat Quality Traits in Chinese Congjiang Xiang and Landrace Pigs by Jiada Yang, Qiaowen Tang, Chunying Sun, Qiuyue Li, Xiaoyu Li, Lu Hou, Yi Yang, Kang Yang

“…PPI network analysis identified <i>PPAR-γ</i> as a central hub gene with 16 direct interactions to other flavor-related genes. (4) Conclusions: These findings demonstrate that the superior meat flavor characteristics of indigenous Chinese pigs are driven by enhanced expression of lipid metabolism genes and distinctive immune-related pathways, providing specific molecular targets for breeding programs aimed at improving meat quality while maintaining production efficiency in commercial breeds.…”
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Hepatic transcriptome profiling unveils candidate genes in cattle with liver abscesses under the influence of beef genetics in dairy cattle. by Luana D Felizari, Sydney M Bowman, Chiquito J Crasto, Jhones O Sarturi, Dale R Woerner, Bradley J Johnson

“…Notably, the most highly up-regulated genes were FGF23, NXPH4, and CYP7A1, while EPHA6, CD70, and INHBA showed the most significant downregulation. …”
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Integrating genome and transcriptome-wide data to explore the expression dynamics of TCP genes in Pisum sativum under salt stress by Song Fangyuan, Li Yong, Jin Huang, Guo Zhiyue, Deng Wen

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Integrated transcriptomic and immune profiling reveals crucial molecular pathways and hub genes associated with postoperative delirium in elderly patients by Zi-han Gou, Nan Su, Xiao-chuan Li, Da-peng Ren, Shan-shan Ren, Lin Wang, Yao Wang

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Transcriptome landscape of the adrenal gland and superior cervical ganglion from hypertension-induced left ventricular hypertrophy rat model by Chaohong Li, Fengting Liu, Xingyu Li, Xiaohua Yang, Qiaoqiao Li, Jing Huang

“…KEGG pathway analysis revealed that the hub genes in the left ventricle and AG were mainly enriched in inflammation-related pathways, while the hub genes in the SCG were primarily enriched in synapse-related pathways. …”
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Dexamethasone’s Clinical Efficacy in Experimental Autoimmune Pancreatitis Correlates with a Unique Transcriptomic Signature, Whilst Kinase Inhibitors Are Not Effective by Ottavia Agrifoglio, Anika Kasprick, Natalie Gross, Marc Wahlig, Emilia Kauffold, Aline Woitas, Artem Vorobyev, Luise Ehlers, Ralf J. Ludwig, Katja Bieber, Robert Jaster

“…In the principal component analysis of pancreatic transcriptomics, poly I:C-injected mice treated with tofacitinib, takinib, or solvent clustered together, while untreated and dexamethasone-treated mice formed separate, unique clusters. (4) Conclusions: Dexamethasone effectively reduced AIP severity, while takinib and tofacitinib were ineffective. …”
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Transcriptomic Profiling Reveals Differences in Slow‐Twitch and Fast‐Twitch Muscles of a Cigarette Smoke‐Exposed Rat Model by Timothy K. H. Fung, Kwok Kuen Cheung, Xia Wang, Benson W. M. Lau, Shirley P. C. Ngai

“…Pathways enrichment analysis revealed that the upregulated pathways in soleus were related to immune system and cellular response, while the downregulated pathways were related to oxidative metabolism. …”
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Organic fertilizer substitution altered the waxy maize grain quality and aroma volatiles formation by the integrated transcriptomic and metabolomic analyses by Xiaoqiang Zhao, Qiang Chai, Wen Yin, Hong Fan, Wei He, Cai Zhao

“…Organic fertilizer substitution is an important agronomic strategy to improve waxy maize quality and aroma, while their regulatory mechanisms remain unclear. …”
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A cross-tissue transcriptome-wide association study identifies WDPCP as a potential susceptibility gene for coronary atherosclerosis by Xinyue Hu, Guanglei Chen, Xiaofang Yang, Jin Cui, Ning Zhang

“…Background: Coronary atherosclerosis (CAS) is a complex chronic inflammatory disease with significant genetic and environmental contributions. While genome-wide association studies (GWAS) have pinpointed many risk loci, over 75 % are in non-coding regions, complicating functional analysis and understanding gene-disease mechanisms. …”
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Single-cell transcriptomic and m6A methylation analyses reveal platelet-mediated immune regulatory mechanisms in sepsis by Weiwei Qian, Yuanyuan Liu, Xinyang Zhao, Yuxin Dong, Jian Zhou, Songtao Shou

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