Characterization of microbial communities in flavors and fragrances during storage by Yingjie Feng, Tingting Zhang, Jinchu Yang, Wenzhao Liu, Yongfeng Yang, Jihong Huang, Shen Huang, Zongcan Yang, Qianjin Liu, Wenchao Zheng, Qing Zhou, Qing Zhou

“…Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database indicated a shift in metabolic pathways within the microbial community, with heightened metabolic activity correlating with spoilage. …”
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Identification of Co-Expression Modules of Cotton Plant Height-Related Genes Based on Weighted Gene Co-Expression Network Analysis by Qian Huang, Li Liu, Hang Li, Xuwen Wang, Aijun Si, Liangrong He, Yu Yu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these modules are associated with biologically significant pathways, including oxidoreductase activity, transcriptional regulator activity, catalytic activity, and phosphate hydrolase activity. …”
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TUBA1B as a novel prognostic biomarker correlated with immunosuppressive tumor microenvironment and immunotherapy response by Juntao Qi, Juntao Qi, Mingming Zhou, Na Yang, Huiyun Ma, Min He, Gujie Wu, Chang Ge, Liuyin Jin, Lin Cheng, Wei Liao, Hefei Ren, Caiyun Lei

“…Despite its fundamental roles, TUBA1B’s impact on tumor prognosis and the tumor immune microenvironment across cancer types remains inadequately understood.Methods To elucidate TUBA1B’s role in cancer prognosis and immune response, we conducted a comprehensive analysis, integrating data from established databases such as The Cancer Genome Atlas, Genotype Tissue Expression, Cancer Cell Lineage Encyclopedia, Human Protein Atlas, Kaplan-Meier Plotter, cBioPortal, TIMER, and ImmuCellAI, along with a large-scale clinical study and immunotherapy cohort. …”
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Comprehensive analysis of mRNA and miRNA differential expression profiles in the hypothalamus-pituitary-gonadal axis in laying and broodiness period of Wanxi white geese by Xinwei Tong, Xiaojin Li, Yuhua Wang, Fei Xie, Ruidong Li, Man Ren, Qianqian Hu, Shenghe Li

“…Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis showed that differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were significantly enriched in hormone level regulation, cell communication, calcium signaling pathway, GnRH signaling pathway, MAPK signaling pathway, Wnt signaling pathway, and other processes. …”
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miR-149-3p Is a Potential Prognosis Biomarker and Correlated with Immune Infiltrates in Uterine Corpus Endometrial Carcinoma by Xiaoyuan Lu, Li Jing, Sicong Liu, Haihong Wang, Buze Chen

“…The TargetScan, PicTar, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to determine the involvement of miR-149-3p target genes in function. …”
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Gastric Cancer Cell Lines Have Different MYC-Regulated Expression Patterns but Share a Common Core of Altered Genes by Jersey Heitor da S. Maués, Helem Ferreira Ribeiro, Giovanny R. Pinto, Luana de Oliveira Lopes, Letícia M. Lamarão, Carla Mariana F. Pessoa, Caroline de Fátima Aquino Moreira-Nunes, Raimundo Miranda de Carvalho, Paulo P. Assumpção, Juan A. Rey, Rommel M. Rodríguez Burbano

“…The DEGs were picked using Sailfish software, followed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using KEGG. …”
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Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia by P. A. Dotsenko, K. A. Zolotareva, R. A. Ivanov, I. V. Chadaeva, N. L. Podkolodnyy, V. A. Ivanisenko, P. S. Demenkov, S. A. Lashin, M. P. Ponomarenko

“…On the evolutionary scale by the Kyoto Encyclopedia of Genes and Genomes (KEGG), the ancestor is the phylum Chordata, some of the most ancient of which evolved the central and the peripheral nervous system. …”
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Absent in melanoma 2: a potent suppressor of retinal pigment epithelial-mesenchymal transition and experimental proliferative vitreoretinopathy by Yu Chen, Mingyuan Jiang, Liping Li, Shanshan Yang, Zuimeng Liu, Shiwen Lin, Wanxiao Wang, Jinyang Li, Feng Chen, Qiang Hou, Xiaoyin Ma, Ling Hou

“…Clinical samples further confirmed the downregulation of AIM2 in the PVR membranes from patients. Kyoto Encyclopedia of Genes and Genome analysis revealed that the PI3K-AKT signaling pathway was significantly related to RPE-EMT and that AIM2 inhibited AKT activation in RPE cells by reducing its phosphorylation. …”
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Involvement of Cholesterol Metabolic Pathways in Recovery from Noise-Induced Hearing Loss by Na Sai, Xi Shi, Yan Zhang, Qing-qing Jiang, Fei Ji, Shuo-long Yuan, Wei Sun, Wei-Wei Guo, Shi-Ming Yang, Wei-Ju Han

“…Both gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses showed that immune and metabolic pathways were prominently involved during the impairment stage of acute hearing loss. …”
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Identification and validation of the important role of KIF11 in the development and progression of endometrial cancer by Biying Wang, Lunmin Bao, Xiaoduo Li, Guang Sun, Wu Yang, Nanzi Xie, Ling Lei, Wei Chen, Hailong Zhang, Man Chen, Xing Zhao, Xiufang Wan, Rui Yuan, Hongmei Jiang

“…Functional enrichment analysis of the DEGs was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. …”
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Transcriptomic and behavioral studies reveal that glutamate receptors are involved in depressive-like behavior in adult olive flounder Paralichthys olivaceus by Liangfang Liu, Tangsong Feng, Mengmeng Shi, Huafeng Zou, Weiqun Lu

“…In addition, Gene Ontology (GO) enrichment analysis revealed that DEGs enriched in peptide biosynthetic process, translation procession were down-regulated in the AG flounder. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that ribosome, oxidative phosphorylation and glutamatergic synapse pathway were over-represented. …”
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Construction of the bromodomain-containing protein-associated prognostic model in triple-negative breast cancer by Wei Chen, Yushuai Yu, Chenxi Wang, Zirong Jiang, Xiewei Huang, Yidan Lin, Hongjing Han, Qing Wang, Hui Zhang

“…Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis were conducted to investigate active pathways and molecular interactions. …”
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A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer by Veronica Rendo, Michael Schubert, Nicholas Khuu, Maria F. Suarez Peredo Rodriguez, Declan Whyte, Xiao Ling, Anouk van den Brink, Kaimeng Huang, Michelle Swift, Yizhou He, Johanna Zerbib, Ross Smith, Jonne Raaijmakers, Pratiti Bandopadhayay, Lillian M. Guenther, Justin H. Hwang, Amanda Iniguez, Susan Moody, Ji-Heui Seo, Elizabeth H. Stover, Levi Garraway, William C. Hahn, Kimberly Stegmaier, René H. Medema, Dipanjan Chowdhury, Maria Colomé-Tatché, Uri Ben-David, Rameen Beroukhim, Floris Foijer

“…We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. Additionally, we analyze 17 cancer open reading frame screens to identify genes toxic to cancer cells when overexpressed. …”
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Comparison of global transcriptomes for nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after their interaction with human intestinal... by Buyandelger Batsaikhan, Pei-Chun Lin, Katsumi Shigemura, Yu-Wei Wu, Reo Onishi, Pei-Ru Chang, Hung-Yen Cheng, Shiuh-Bin Fang

“…Certain Salmonella Pathogenicity Island (SPI)-1 genes (sipC, sipA, sicA, sipD, and sipB), SPI-2 genes (ssaP, ssrA, and ssaS), and six SPI-4 genes (siiA, siiB, siiC, siiD, siiE, and siiF) remained upregulated in the bacteremic blood-derived strains but significantly downregulated in the nonbacteremic strains after their interaction with Caco-2 cells. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified that arginine biosynthesis, ascorbate and aldarate metabolism, and phosphotransferase system pathways were activated in bacteremic NTS strains after Caco-2 cell priming. …”
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Identification of EARS2 as a Potential Biomarker with Diagnostic, Prognostic, and Therapeutic Implications in Colorectal Cancer by Wang L, Deng X, Tang J, Gong Y, Bu S, Li Z, Liao B, Ding Y, Dai T, Liao Y, Li Y

“…To investigate the mechanisms underlying EARS2 in CRC, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis, and Protein-Protein Interaction analyses were performed, alongside the construction of miRNA-mRNA interaction networks. …”
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Transcriptomic and metabolomic-based revelation of the effect of fresh corn extract on meat quality of Jingyuan chicken by Jinli Tian, Yanxu Wu, Wei Zhao, Guojun Zhang, Hu Zhang, Lin Xue, Lijuan Yang, Tong Zhang, Yaling Gu, Juan Zhang

“…Gene Ontology (GO) analyses of DEGs indicate multiple entries involved in IMF synthesis such as skeletal system development and cellular response to amino acid stimulation. Kyoto Encyclopedia of Genes and Genomes (GSEA-KEGG) analysis identified sphingolipid_metabolism and multiple genes affecting IMF deposition including SPHK1, CERS1, CERS6, GLB1L, SGMS2, UGT8, and UGCG. …”
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Correlation analysis of the impact of Clonorchis sinensis juvenile on gut microbiota and transcriptome in mice by Xueling Deng, Shitao Li, Yuhong Wu, Jiali Yao, Wei Hou, Jiangyao Zheng, Boying Liang, Xiaole Liang, Qiping Hu, Zhanshuai Wu, Zeli Tang

“…Enriched Gene Ontology items highlighted immune and detoxification-related processes, including immunoglobulin production and xenobiotic metabolic processes. Kyoto Encyclopedia of Genes and Genomes pathway analysis further indicated involvement in circadian rhythm, as well as various detoxification and metabolic-related pathways (e.g., glutathione metabolism and glycolysis/gluconeogenesis). …”
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Effect of remote ischemic preconditioning on perioperative neurocognitive disorder in elderly patients undergoing major surgery and associated genetic variant analysis: a randomize... by Feifei Xu, Tingting Liu, Huiqing Liu, Jiao Deng, Shan He, Zhihong Lu, Haopeng Zhang, Hailong Dong

“…A total of 3877 mutated genes were exclusively identified in PND patients. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these mutated genes are enriched in synapse function. …”
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Identification of a transcription factor AoMsn2 of the Hog1 signaling pathway contributes to fungal growth, development and pathogenicity in Arthrobotrys oligospora by Qianqian Liu, Kexin Jiang, Shipeng Duan, Na Zhao, Yanmei Shen, Lirong Zhu, Ke-Qin Zhang, Jinkui Yang

“…Furtherly, we analyzed the protein interaction network of AoMsn2 based on the Kyoto Encyclopedia of Genes and Genomes pathway map and the online website STRING. …”
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Full-length transcriptome analysis of male and female gonads in Japanese Eel (Anguilla japonica) by Jiangling Li, Jingjie Liang, Mengyang Wang, Yuewen Jiang, Wen Li, Mingxi Huang, Yan Huang, Yangjie Xie, Jianchun Chen, Tiansheng Chen

“…Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed significant pathways involved in cell cycle regulation, metabolic processes, apoptosis, and hormone activity. …”
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