Nuclear-localized HKDC1 promotes hepatocellular carcinoma through phosphorylating RBBP5 to upregulate H3K4me3 by Ling Ye, Shengqi Shen, Qiankun Mao, Hui Lu, Haiying Liu, Pinggen Zhang, Zetan Jiang, Wenhao Ma, Yuchen Sun, Yiyang Chu, Zilong Zhou, Rui Liu, Jian Li, Shi-ting Li, Ping Gao, Huafeng Zhang

“…These findings highlight the protein kinase function of HKDC1 in the activation of H3K4me3, gene expression, and HCC progression.…”
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Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum by Saixian Zhang, Yue Xiang, Yaobang Jian, Qiulin Zhao, Jiahui Sun, Yi Huang, Jing Xu, Xiaolong Qi, Jingjin Li, Zhuqing Zheng, Liangliang Fu, Yuwen Liu, Xinyun Li

“…To explore the genetic and regulatory mechanisms behind FE, we conducted an integrative multi-omics study using RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on pigs with high and low FE. By comparing gene expression and chromatin accessibility profiles in the jejunum, we identified key differentially expressed genes (DEGs) and differentially accessible regions (DARs) associated with lipid metabolism and immune function, both of which are critical pathways for efficient growth. …”
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A prognostic model of 8-T/B cell receptor-related signatures for hepatocellular carcinoma by Xuan Zuo, Hui Li, Shi Xie, Mengfen Shi, Yujuan Guan, Huiyuan Liu, Rong Yan, Anqi Zheng, Xueying Li, Jiabang Liu, Yifan Gan, Haiyan Shi, Keng Chen, Shijie Jia, Guanmei Chen, Min Liao, Zhanhui Wang, Yanyan Han, Baolin Liao

“…Methods In this study, we categorized gene expression data of HCC patients from The Cancer Genome Altas and identified TCR related genes by the Least Absolute Shrinkage and Selection Operator and multivariate Cox regression analysis. …”
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Qualitative and quantitative characteristics of black patch trait in Oujiang color common carp by Ke Jing, Huifan Chen, Nusrat Hasan Kanika, Penghui Zhang, Roland Nathan Mandal, Chunxiao Zeng, Zhiyi Zhang, Jun Wang, Chenghui Wang

“…Furthermore, the six relative gene expression levels of the melanogenesis pathway, Ednrb, Tyr, Tyrp1, Mc1r, Kit and Asip, in the skin of the hybrid were between the parent RB and WW. …”
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Coordinated neuron-specific splicing events restrict nucleosome engagement of the LSD1 histone demethylase complex by Robert S. Porter, Sojin An, Maria C. Gavilan, Masayoshi Nagai, Yumie Murata-Nakamura, Bo Zhou, Katherine M. Bonefas, Olivier Dionne, Jeru Manoj Manuel, Joannie St-Germain, Suzanne Gascon, Jacqueline Kim, Liam Browning, Benoit Laurent, Uhn-Soo Cho, Shigeki Iwase

“…The neuronal PHF21A, albeit with its weaker nucleosome binding, is necessary for normal gene expression and the H3K4 landscape in the developing brain. …”
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Genome-wide identification and expression analysis of phytochrome gene family in Aikang58 wheat (Triticum aestivum L.) by Zhu Yang, Zhu Yang, Wenjie Kan, Wenjie Kan, Ziqi Wang, Caiguo Tang, Yuan Cheng, Yuan Cheng, Dacheng Wang, Dacheng Wang, Yameng Gao, Lifang Wu, Lifang Wu

“…., which are mainly involved in plant development, hormone response, and stress response. Gene expression profiling demonstrated that TaAkPHY genes exhibit varying expression levels across different tissues and are induced by various stress conditions and plant hormone treatments. …”
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Identification and expression analysis of c-type and g-type lysozymes genes after Aeromonas hydrophila infection in African catfish by Hasan Nasrullah, Yanti Inneke Nababan, Dwi Hany Yanti, Dian Hardiantho, Sri Nuryati, Muhammad Zairin Junior, Julie Ekasari, Alimuddin Alimuddin

“…Keywords: lysozymes, gene identification, gene expression, bacterial infection, African catfish   ABSTRAK Lisozim berperan dalam sistem pertahanan dini pada ikan dan sangat potensial digunakan sebagai marka status imunitas dalam evaluasi respons imun. …”
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Mina53 catalyzes arginine demethylation of p53 to promote tumor growth by Lixiao Zhou, Liyang Yu, Shushu Song, Yong Wang, Qiang Zhu, Meng Li, Yutong Sha, Liang Xu, Xin Shu, Qingqing Liao, Ting Wu, Bing Yang, Siyuan Chai, Bingyi Lin, Liming Wu, Ruhong Zhou, Xiaotao Duan, Chenggang Zhu, Yuanyuan Ruan, Wen Yi

“…Moreover, downregulation of p53-mediated gene expression is observed in several types of cancer with elevated expression of Mina53. …”
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OsLAP3/OsSTRL2, encoding a rice strictosidine synthase, is required for anther cuticle formation and pollen exine patterning in rice by Dai-bo Chen, Ran Zhou, Ran Zhou, Hui-min Wang, Pei-pei Zhang, Zheng-fu Yang, Zheng-fu Yang, Dan-dan Xuan, Ying-xin Zhang, Xiao-deng Zhan, Li-yong Cao, Li-yong Cao, Shi-hua Cheng, Lian-ping Sun, Lian-ping Sun

“…OsLAP3 is homologous to the maize ZmMS45, the core recessive nuclear sterile gene of maize Seed Production Technology (SPT), and localizes to the endoplasmic reticulum and plays a conserved role in anther development and pollenformation. Gene expression analysis revealed a significant downregulation of key genes involved in anther development and sporopollenin biosynthesis in lap3 anthers. …”
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Col1A1 as a new decoder of clinical features and immune microenvironment in ovarian cancer by Xiao Xiao, Fangyi Long, Shaolan Yu, Wengjuan Wu, Dayan Nie, Xiaoyan Ren, Wen Li, Xujuan Wang, Ling Yu, Pinghan Wang, Gang Wang

“…The LinkedOmics and INPUT2 databases were used to analyze differential gene expression in OC, This was followed by enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) annotations to identify and predict potential signaling pathways associated with COL1A1.ResultsOur study demonstrated that COL1A1 expression was significantly elevated in OC tissues compared to normal ovarian tissues. …”
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Exploring the Potential of Malvidin and Echiodinin as Probable Antileishmanial Agents Through In Silico Analysis and In Vitro Efficacy by Luis Daniel Goyzueta-Mamani, Daniela Pagliara Lage, Haruna Luz Barazorda-Ccahuana, Margot Paco-Chipana, Mayron Antonio Candia-Puma, Gonzalo Davila-Del-Carpio, Alexsandro Sobreira Galdino, Ricardo Andrez Machado-de-Avila, Rodolfo Cordeiro Giunchetti, Edward L. D’Antonio, Eduardo Antonio Ferraz Coelho, Miguel Angel Chávez-Fumagalli

“…The in silico analysis revealed strong binding between malvidin and <i>Leishmania</i> arginase, with the residues HIS139 and PRO258 playing key roles. Gene expression analysis indicated malvidin’s modulation of oxidative stress and DNA repair pathways, involving genes like GLO1 and APEX1. …”
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Characterization of a novel covS SNP identified in Australian group A Streptococcus isolates derived from the M1UK lineage by Johanna Richter, Amanda J. Cork, Yvette Ong, Nadia Keller, Andrew J. Hayes, Mark A. Schembri, Amy V. Jennison, Mark R. Davies, Kate Schroder, Mark J. Walker, Stephan Brouwer

“…Site-directed mutagenesis was performed to assess the impact of this mutation on virulence and global gene expression. We found that the CovSAla318Val mutation led to subtle, virulence-specific changes of the CovRS regulon compared to previously characterized covS mutations, highlighting an unappreciated level of complexity in CovRS-dependent gene regulation. …”
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MLL4 regulates postnatal palate growth and midpalatal suture development by Jung-Mi Lee, Hunmin Jung, Bruno de Paula Machado Pasqua, Yungki Park, Qinghuang Tang, Shin Jeon, Shin Jeon, Soo-Kyung Lee, Jae W. Lee, Hyuk-Jae Edward Kwon

“…Using micro-computed tomography (CT), histological analysis, cell mechanism assays, and gene expression profiling, we examined palate development and growth in the Mll4-cKO mice. …”
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Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to <i>Rhizoctonia solani</i> under excess nitrogen fertili... by E. A. Antropova, A. R. Volyanskaya, A. V. Adamovskaya, P. S. Demenkov, I. V. Yatsyk, T. V. Ivanisenko, Y. L. Orlov, Ch. Haoyu, M. Chen, V. A. Ivanisenko

“…A comprehensive bioinformatics approach was applied, including differential gene expression analysis, gene network reconstruction, biological process overrepresentation analysis, phylostratigraphic analysis, and non-coding RNA co-expression analysis. …”
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Effect of prolonged starvation on nutrition utilization and transcriptional responses in Pacific oyster (Crassostrea gigas) by Mingkun Liu, Chenchen Wei, Wenwen Xu, Lintao Tan, Li Li, Guofan Zhang

“…Combined with the correlation between gene expression and symbiotic microbiota, these findings indicated that oysters, due to limited energy, activated insufficient immune responses, leading to increased pathogen abundance and higher mortality during prolonged starvation. …”
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Gene networks for use in metabolomic data analysis of blood plasma from patients with postoperative delirium by V. A. Ivanisenko, N. V. Basov, A. A. Makarova, A. S. Venzel, A. D. Rogachev, P. S. Demenkov, T.  V. Ivanisenko, M. A. Kleshchev, E. V. Gaisler, G. B. Moroz, V. V. Plesko, Y. S. Sotnikova, Y. V. Patrushev, V. V. Lomivorotov, N. A. Kolchanov, A. G. Pokrovsky

“…Within this set, 47 are assumed to be regulators of gene expression, governing the transcription of enzymes pivotal to the metabolic cascade. …”
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Identification of common and specific fibrosis-related genes in three common chronic kidney diseases by Zhangning Fu, Xiaodong Geng, Chao Liu, Wanjun Shen, Zheyi Dong, Guannan Sun, Guangyan Cai, Xiangmei Chen, Quan Hong

“…Background Kidney fibrosis is the common final pathway of virtually all advanced forms of chronic kidney disease (CKD) including diabetic nephropathy (DN), IgA nephropathy (IgAN) and membranous nephropathy (MN), with complex mechanism. Comparative gene expression analysis among these types of CKD may shed light on its pathogenesis. …”
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Dynamics and regulatory roles of RNA m6A methylation in unbalanced genomes by Shuai Zhang, Ruixue Wang, Kun Luo, Shipeng Gu, Xinyu Liu, Junhan Wang, Ludan Zhang, Lin Sun

“…N6-methyladenosine (m6A) in eukaryotic RNA is an epigenetic modification that is critical for RNA metabolism, gene expression regulation, and the development of organisms. …”
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Melanin-like nanoparticles slow cyst growth in ADPKD by dual inhibition of oxidative stress and CREB by Yongzhan Sun, Quan Zou, Huizheng Yu, Xiaoping Yi, Xudan Dou, Yu Yang, Zhiheng Liu, Hong Yang, Junya Jia, Yupeng Chen, Shao-Kai Sun, Lirong Zhang

“…Mechanistically, we observed that MMPP directly binds to the bZIP DNA-binding domain of CREB, leading to competitive inhibition of CREB’s DNA binding ability and subsequent reduction in CREB target gene expression. In summary, our findings identify an intracellular target of MMPP and demonstrate its potential for treating ADPKD by simultaneously targeting oxidative stress and CREB transcriptional activity.…”
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Titin gene mutations enhance radiotherapy efficacy via modulation of tumour immune microenvironment in rectum adenocarcinoma by Hengchang Liu, Jialiang Liu, Xu Guan, Zhixun Zhao, Pu Cheng, Haipeng Chen, Zheng Jiang, Xishan Wang

“…Abstract Objective This study investigates the impact of Titin (TTN) gene mutations on radiotherapy sensitivity in rectum adenocarcinoma (READ) by examining changes in the tumour immune microenvironment. Methods Data on gene expression and mutations in READ were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. …”
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