Removal of dissolved organic carbon in the West Pacific hadal zones by Mengfan Chu, Rui Bao, Michael Strasser, Ken Ikehara, Yang Ding, Kejian Liu, Mingzhi Liu, Li Xu, Yonghong Wang, Piero Bellanova, Troy Rasbury, Martin Kölling, Natascha Riedinger, Min Luo, Christian März, Kana Jitsuno, Zhirong Cai, Cecilia McHugh, Ellen Druffel

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Protective effect and mechanism of Sufentanil on acute lung injury in septic mice by Hongqiao Hou, Bowen Jiang, Aiqing Zhu, Junjun Hou, Zhe Qu, Ruping Liu, Aiqun Li

“…To this end, a protein-protein interaction (PPI) network for common targets was first constructed with Swiss Target Prediction Database, GeneCards Database, Draw Venn Diagram Software, STRING 11.5 Database, Cytoscape 3.10.0 Software and Metascape Database, and then key targets were subject to enrichment analysis by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to obtain the key targets of Sufentanil for the treatment of pulmonary sepsis, and then verified by animal experiments. …”
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Puerarin Ameliorates the Ferroptosis in Diabetic Liver Injure Through the JAK2/STAT3 Pathway Inhibition Based on Network Pharmacology and Experimental Validation by Fan X, Liu S, Yu J, Hua J, Feng Y, Wang Z, Shen Y, Lan W, Wang J

“…Protein-protein interaction (PPI) network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to predict key targets and pathways. …”
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Identification of Potential miRNA-mRNA Regulatory Network Contributing to Parkinson’s Disease by Xi Yin, Miao Wang, Wei Wang, Tong Chen, Ge Song, Yixuan Niu, Ziying Jiang, Zhongbao Gao, Zhenfu Wang

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then conducted by Database for Annotation, Visualization and Integrated Discovery (DAVID) and Metascape analytic tools. …”
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Synergistic interaction between wheat streak mosaic virus and Triticum mosaic virus modulates wheat transcriptome to favor disease severity by Haritha Nunna, Nathan A. Palmer, Gautam Sarath, Stephen N. Wegulo, Satyanarayana Tatineni, Satyanarayana Tatineni

“…Gene ontology, protein domain and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that genes specifically related to photosynthesis, growth, stress, senescence, and defense were differentially enriched. …”
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Identification of immune-associated genes with altered expression in the spleen of mice enriched with probiotic species using RNA-seq profiling by Anh Duc Truong, Ha Thi Thanh Tran, Nhu Thi Chu, Lanh Phan, Hoai Thi Phan, Thu Huong Dang, Hoang Vu Dang, La Anh Nguyen

“…On the other hand, 12 toll-like receptor genes underwent additional validation through quantitative real-time polymerase chain reaction (qRT-PCR), affirming the increased alignment between qRT-PCR and RNA-Seq findings. In addition, the Kyoto encyclopedia of genes and genomes and gene ontology analyses revealed that the DEGs were predominantly enriched in defense responses to pathogens, including inflammatory bowel diseases, malaria, leukaemia virus 1, and herpes virus, as well as immune processes related to immune response and signal transduction. …”
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TOM40 as a prognostic oncogene for oral squamous cell carcinoma prognosis by Lifei Deng, Hong Ran, Dunhui Yang, Zhen Wang, Peng Zhao, Hengjie Huang, Yongjin Wu, Peng Zhang

“…A network of genes co-expressed with TOM40 was constructed and functionally annotated by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. …”
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Identification and Analysis of Potential Immune-Related Biomarkers in Endometriosis by Yanan He, Jixin Li, Yanjun Qu, Liyuan Sun, Xibo Zhao, Han Wu, Guangmei Zhang

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DETFs and DEIRGs. …”
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Current concepts of chronic gastritis and gastropathies: new international consensus RE.GA.IN by S.M. Tkach, N.V. Kharchenko, A.E. Dorofieiev, Yu.Z. Hurkalo, L.M. Ryzhiy

“…In addition to the Sydney and Houston gastritis classifications, the six editions of the Maastricht Consensus (1996–2022) and the Kyoto Global Consensus deserve special attention, thanks to which broad agreements and significant scientific achievements became possible in the most controversial issues of the entire spectrum of gastritis, with a special emphasis on H.pylori gastritis, which accounts for more than 90 % of all forms of gastritis worldwide. …”
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CircRNA-miRNA-mRNA regulatory network in high-altitude hypobaric hypoxia-induced hearing impairment and hearing acclimatization by Danzeng Awang, Kanzi Danzeng, Tianheng Wang, Quzong Deji, Mengting Huang, Hailong Ren, Xinzhu Liu, Binghan Zhao, Lanzi Gongga

“…The DEmRNAs in this network were functionally annotated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses based on Metascape. …”
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Transcriptome Analysis of Effect of Cordyceps militaris Aqueous Extract in Human Gastric Cancer Cell BGC-823 on Different RCD Pathways by Mingqi CUI, Kaiwen YU, Yang SONG, Fangxu XU, Shenghou WANG, Ze WANG

“…Transcriptome analysis revealed significant differentially expressed genes (DEGs) and their Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, resulting in the identification of 10 hub genes involved in the apoptosis, autophagy, necroptosis, and ferroptosis signaling pathways. …”
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Effects of hypoxia on the heart of the juvenile four-finger threadfin (Eleutheronema tetradactylum) based on physiological indicators and transcriptome analysis by Yi Lu, Eric Amenyogbe, Ye- Yang, Zhong-liang Wang, Zhong-liang Wang, Zhong-liang Wang, Jing-hui Jin, Rui-tao Xie, Eric Kwabena Droepenu, Jian-sheng Huang, Jian-sheng Huang, Jian-sheng Huang

“…Transcriptome analysis identified upregulated genes involved in cell communication, immune responses, and intracellular signaling, offering potential targets for breeding hypoxia-tolerant species. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis highlighted key pathways such as mitogen-activated protein kinase (MAPK), hypoxia-inducible factor-1 (HIF-1), endocytosis, and phagosome formation. …”
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Untangling the complex mechanisms associated with Alzheimer's disease in elderly patients using high-throughput RNA sequencing data and next-generation knowledge discovery methods:... by Hind A. Alkhatabi, Peter Natesan Pushparaj

“…We used NGKD tools such as GEO RNA-seq Experiments Interactive Navigator (GREIN) to obtain differentially expressed genes (DEGs) by comparing the AD versus Old RNA-seq data and further filtered and normalized to obtain differentially regulated Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome and Panther pathways using ExpressAnalyst tool. …”
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A Proteomic Study Based on Home Quarantine Model Identifies NQO1 and Inflammation Pathways Involved in Adenoid Hypertrophy by Chen P, Hou S, Pang X, Li L, Wei W

“…Differences in protein expression were analyzed using Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis, Protein-protein interaction, and immunohistochemistry analysis.Results: Long-term home quarantine had a profound impact on the proteomics of pediatric adenoids, with up-regulated and down-regulated proteins of 28 and 92 downregulated proteins, respectively. …”
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Identification of Anoikis-Related Genes in Chronic Kidney Disease Based on Bioinformatics Analysis Combined with Experimental Validation by Liu H, Mei M, Zhong H, Lin S, Luo J, Huang S, Zhou J

“…We aimed to establish the Anoikis-related gene signature in CKD by bioinformatics analysis.Methods: We retrieved 3 datasets from the Gene Expression Omnibus (GEO) database to obtain differentially expressed genes (DEGs), followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) of them, which were intersected with Anoikis-related genes (ARGs) to derive Anoikis-related differentially expressed genes (ARDEGs). …”
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Association between gut microbiota and short-chain fatty acids in children with obesity by Shihan Li, Xinyu Ma, Hong Mei, Xuening Chang, Peiling He, Lingli Sun, Han Xiao, Shiqiong Wang, Ruizhen Li

“…Caproate levels significantly increased, whereas butyrate and isobutyrate levels decreased in children in the OG than those in the NG. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis revealed 28 enriched KEGG pathways, of which/with the phosphotransferase system (PTS) and enhanced biofilm formation by Escherichia coli were particularly significant in the OG. …”
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Effect of Acetyl tributyl citrate on bone metabolism based on network toxicology and molecular docking technology by Xuan Lin, Kun Lin, Yue Lai, Qingping Peng, Miao Xu, Yiting Xu, Jialin Yang, Huan Liu, Jianlin Shen

“…In-depth Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, conducted within the Metascape database, revealed that the core targets of ATBC’s influence on bone metabolism are predominantly concentrated within vital signaling cascades, including thyroid hormone signaling, FOXO signaling, glucagon signaling, AMPK signaling, insulin signaling, adipocytokine signaling, and Notch signaling pathways. …”
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Immune regulatory genes impact the hot/cold tumor microenvironment, affecting cancer treatment and patient outcomes by Mengmeng Sang, Jia Ge, Juan Ge, Juan Ge, Gu Tang, Qiwen Wang, Jiarun Wu, Liming Mao, Liming Mao, Xiaoling Ding, Xiaorong Zhou

“…A customized immunogram was created to identify important immunological characteristics. Kyoto Encyclopedia of Genes and Genomes and Hallmark pathway enrichment were evaluated through gene set variation analysis. …”
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In silico analysis of hub genes and regulatory networks implicates the putamen in non-motor Parkinson’s disease disorders by Stephen Tunmise Akanbi, Joshua Ayodele Yusuf, Thompson Oluwaferanmi Ayandele, Dayo Samson Oladipupo, Darasimi Racheal Olorunlowu, Blessing Dorcas Olawuyi, Joshua Oluwafisayo Adepoju, Dolapo Emmanuel Opasina, Elizabeth Kehinde Opoola, Uchenna Victor Ugwuanyi, Olufunto Omodele Adeleye

“…Enrichment analysis of target genes was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Also, we constructed transcription factor (TF)-hub gene expression networks, miRNA-hub gene expression networks, and disease hub gene association networks using the JASPAR database, Tarbase database, and DisGeNET via NetworkAnalyst platform, respectively. …”
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The dual anti-inflammatory and anticoagulant effects of Jianpi Huashi Tongluo prescription on Rheumatoid Arthritis through inhibiting the activation of the PI3K/AKT signaling pathw... by Fanfan Wang, Fanfan Wang, Jian Liu

“…Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results suggested that the pharmacodynamic mechanism of XFC may be closely related to the regulation of the PI3K/AKT signaling pathway. …”
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