Genome-wide identification and expression analysis of growth-regulating factor (GRF) and GRF-interacting factor (GIF) gene families in Castanea mollissima by WANG Xiangyu, TIAN Yujuan, LI Yun, WANG Dongsheng, WANG Xuan, GUO Chunlei, LIU Jing, ZHANG Hai’e, ZHANG Jingzheng, YU Liyang

“…Transcriptome data analysis showed that CmGRF3 and CmGIF2 were consistently highly expressed in female flowers, while almost not in male flowers (FPKM<1). …”
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Anthocyanin Degradation Drives Heat-Induced Petal Fading in <i>Chrysanthemum morifolium</i> at Full Bloom: A Multi-Omics Analysis by Ge Zhao, Yanan Li, Jialin Peng, Xiuge Li, Wenhao Xia, Yuhe Tian, Yukun Li, Lijie Zhou

“…Transcriptomic analysis identified nine core structural genes and three key transcription factors involved in anthocyanin biosynthesis, along with twelve core genes linked to enzymatic anthocyanin degradation. …”
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Genome-wide characterization and expression profiling of MADS-box family genes during organ development and drought stress in Camelina sativa L by Somayeh Tahmasebi, Parisa Jonoubi, Mohammad Majdi, Ahmad Majd, Parviz Heidari

“…The predicted molecular weights (MW) of the CsMADS-box proteins displayed a range from 17.01 to 94.06 kDa, while the isoelectric points (pI) were observed to span from 4.13 to 10.09. …”
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TMEM132A: a novel susceptibility gene for lung adenocarcinoma combined with venous thromboembolism identified through comprehensive bioinformatic analysis by Pei Xie, Yingli Liu, Pingping Bai, Yue Ming, Qi Zheng, Li Zhu, Yong Qi

“…Therapeutic potential was assessed via DSigDB-based drug sensitivity profiling.ResultThrough transcriptomic analysis, we identified 381 CGs, which demonstrated significant enrichment in inflammatory cascades, immunological processes, and coagulation pathways. …”
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Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer by Tianle Xue, Yunpeng Chen, Xiaomeng Li, Zhixiang Zhou, Qiyang Chen

“…In addition, immune cell infiltration, protein–protein interaction (PPI) networks, and drug enrichment analyses—including molecular docking—were performed to further elucidate the biological functions and therapeutic potentials of the identified genes.ResultsOur analysis revealed significant transcriptomic alterations in UC and CRC tissues, with the turquoise module demonstrating the strongest association with disease traits. …”
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Cross-species single-cell RNA-seq analysis reveals disparate and conserved cardiac and extracardiac inflammatory responses upon heart injury by Eric Cortada, Jun Yao, Yu Xia, Friederike Dündar, Paul Zumbo, Boris Yang, Alfonso Rubio-Navarro, Björn Perder, Miaoyan Qiu, Anthony M. Pettinato, Edwin A. Homan, Lisa Stoll, Doron Betel, Jingli Cao, James C. Lo

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Multi-omics analysis reveals the role of the autophagy-related gene AGT in chemotherapy resistance in colorectal cancer and the therapeutic potential of its inhibitors by Wenjiao Cai, Tao Xiang, Xiaoli Liu, Chong Fu

“…Drug sensitivity analysis was conducted based on the CTRP database, while immune infiltration was assessed using the CIBERSORT and ESTIMATE methods. …”
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Metabolomic and evolutionary integration unveils medicinal potential in six Corydalis species by Yun Gao, Xiangyu Zhou, Mengxiao Yan, Zhengwei Wang, Xin Zhong, Xiaochen Li, Junjie Zhu, Yu Kong, Wanrong Zhu, Ruolin Geng, Yaping Zhou, Qing Zhao, Yonghong Hu, Ping Xu

“…In this study, we conducted an integrated evolutionary analysis by combining whole-genome resequencing with comprehensive metabolite profiling across various Corydalis species. …”
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Astaxanthin mitigates doxorubicin-induced cardiotoxicity via inhibiting ferroptosis and autophagy: a study based on bioinformatic analysis and in vivo/vitro experiments by Bowen Yin, Jingyi Ren, Xuanyi Liu, Yadong Zhang, Jinshi Zuo, Rui Wen, Huanting Pei, Miaomiao Lu, Siqi Zhu, Zhenao Zhang, Ziyi Wang, Yanyi Zhai, Yuxia Ma

“…Specifically, ASX upregulates solute carrier family 7 member 11 (SLC7A11) and glutathione peroxidase 4 (GPX4), while downregulating the expression of transferrin receptor 1 (TFRC), ferritin heavy chain (FTH1) and ferritin light chain (FTL). …”
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The systematic analysis of genes related to butyrate metabolism suggests that CDKN3 could serve as a promising therapeutic target for lung adenocarcinoma treatment by Yanchao Luan, Chao Liang, Qingsong Han, Xueqin Zhou, Na Yang, li Zhao

“…Results Through a comprehensive analysis of the TCGA-LUAD dataset, 51 significant BMR-DEGs were confirmed. …”
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Epitranscriptomic Analysis of the Ventral Hippocampus in a Mouse Model of Post-Traumatic Stress Disorder Following Deep Brain Stimulation Treatment of the Basolateral Amygdala by Mingxi Ma, Hao Fan, Hui Zhang, Yao Yin, Yizheng Wang, Yan Gao

“…Gene ontology (GO) enrichment analysis revealed that FS altered methylation in metabolic, developmental, and cytoskeletal pathways, while BLA DBS targeted metabolic, cell cycle, and neuroplasticity-related genes. …”
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Study on factors affecting fruit development of seedless ponkan cultivar Huagan No.4 by LIU Chenglang, LI Gangqiu, LI Shunxin, WEI Ranran, LU Yan, CHENG Chao, TANG Zheng, LIU Baoyan, YE Junli, CHAI Lijun, DENG Xiuxin, XIE Zongzhou

“…The GA3 content of HG2 peaked at 2.27 ng·g-1 on 25 DAF, while the GA3 content of HG4 was only 0.90 ng·g-1, with significant differences. …”
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Behavioral assessment and gene expression changes in a mouse model with dysfunctional STAT1 signaling by Luca Büschgens, Nina Hempel, Aditi Methi, Andre Fischer, Nele Siering, Lars Piepkorn, Olaf Jahn, Thomas Meyer, Oliver Wirths

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Prognostic and tumor microenvironmental features of gastric cancer revealed by macrophage polarization and protein lactylation-related genes by Zifan Xu, Zifan Xu, Zi Lei, Shilan Peng, Sha Li, Dehui Kong, Hongqiong Duan, Man Zhang, Guomiao Su, Guoqing Pan

“…ERCC6L is located on chromosome X, while MYB is located on chromosome 6. Gene-gene interaction network analysis revealed interactions between prognostic genes and other key genes. …”
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Shared and specific competing endogenous RNAs network mining in four digestive system tumors by Yulai Tang, Aamir Fahira, Siying Lin, Yiming Shao, Zunnan Huang

“…Functional enrichment analysis and prognostic RNA screening were performed with ConsensusPathDB and univariate Cox regression analysis. …”
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Induced collagen type‐I secretion by hepatocytes of the melanoma liver metastasis is associated with a reduction in tumour‐infiltrating lymphocytes by Shodai Mizuno, Matias A. Bustos, Yoshinori Hayashi, Kodai Abe, Satoru Furuhashi, Yalda Naeini, Xiaowei Xu, Anton J Bilchik, Dave S. B. Hoon

“…Validation was performed using multiplex immunofluorescence. Results In NGDSP analysis adjacent normal hepatocytes (ANH) had higher CXCR4 and COL1A1/2 levels than distant normal hepatocytes (DNH), while melanoma cells had higher TNF‐α levels. …”
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Isodon lophanthoides alleviates liver fibrosis via modulation of purine metabolism and NF-κB signaling pathway: insights from multi-omics analysis by Kuikui Chen, Kuikui Chen, Kuikui Chen, Jie Liang, Jie Liang, Yong Tan, Yong Tan, Yaohua Li, Xiaojiao Pan, Xiaojiao Pan, Zhonghui Guo, Zhonghui Guo, Wentao Zhang, Zongxi Sun

“…High-dose ILW lowered hepatic levels of adenine, adenosine monophosphate (AMP), and inosine monophosphate (IMP), while increasing adenosine, hypoxanthine, and N6-methyladenosine (m6A). …”
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Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire. by Ivy K Brown, Nathan Dyjack, Mindy M Miller, Harsha Krovi, Cydney Rios, Rachel Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P O'Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A Seibold, James Scott-Browne, Radleigh G Santos, R Lee Reinhardt

“…Antigen-reactivity of the broader repertoires was predicted to be shared across both tissues and individual mice. Transcriptome, trajectory, and chromatin accessibility analysis of lung and lymph-node repertoires revealed three unique but related populations of responding IL-4+ CD4+ T cells consistent with T follicular helper, T helper 2, and a transitional population sharing similarity with both populations. …”
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Antiaging Effect of 2-<i>O</i>-β-D-Glucopyranosyl Ascorbic Acid Derived from <i>Lycium barbarum</i> L. Through Modulating the IIS Pathway and Gut Microbiota in <i>Caenorhabditis el... by Jiayue Fang, Wei Dong, Jingqian Zheng, Boxuan Han, Yuying Zhang, Jianing Wang, Xiaoxiong Zeng

“…It significantly extended their lifespan, enhanced stress resistance, reduced lipofuscin accumulation, and improved their healthspan, while strengthening antioxidant defenses. Transcriptomic analysis identified the insulin/insulin-like growth factor (IGF)-1 signaling pathway as a key regulator, with quantitative real-time polymerase chain reaction confirming the upregulation of longevity-associated genes. …”
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Meta_B cells: a computationally identified candidate immunosuppressive driver of gastric cancer metastasis revealed by single-cell analysis and machine learning by Tianchi Lei, Yiwen Jiang, Kexin Yang, Chuqi Meng, Yue An

“…Abstract Background Gastric cancer (GC) metastasis remains a major clinical challenge due to insufficient understanding of tumor microenvironment (TME) dynamics. While B cells are implicated in GC progression, their subset-specific roles in metastatic niches are poorly defined. …”
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