Screening and Functional Pathway Analysis of Pulmonary Genes Associated with Suppression of Allergic Airway Inflammation by Adipose Stem Cell-Derived Extracellular Vesicles by Sung-Dong Kim, Shin Ae Kang, Yong-Wan Kim, Hak Sun Yu, Kyu-Sup Cho, Hwan-Jung Roh

“…Enrichment analysis based on the Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were also performed to further identify the function of DEGs. …”
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The heterogeneity of NOTCH1 to tumor immune infiltration in pan-cancer by XiaoJun Duan, Rihan Wu, Mingyang Zhang, Kexin Li, Lei Yu, Huirong Sun, Xingxia Hao, Changshan Wang

“…NOTCH1 expression was significantly up-regulated in cold tumors but down-regulated in hot tumors. The Gene ontology (GO) enrichment analysis of NOTCH1 with the two categories placed stress on angiogenesis and protein dealkylation, respectively. …”
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In ovo delivery of carvacrol triggers expression of chemotactic factors, antimicrobial peptides and pro-inflammatory pathways in the yolk sac of broiler chicken embryos by Mila M. Y. Meijer, Henry van den Brand, Shahram Niknafs, Eugeni Roura

“…Functional analyses of these differentially expressed genes, using KEGG, REACTOME, and Gene Ontology databases, showed enrichment of several immune-related pathways. …”
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Integrated Bioinformatics-Based Identification of Potential Diagnostic Biomarkers Associated with Diabetic Foot Ulcer Development by Long Qian, Zhipeng Xia, Ming Zhang, Qiong Han, Die Hu, Sha Qi, Danmou Xing, Yan Chen, Xin Zhao

“…These DEGs were then arranged into a protein-protein interaction (PPI) network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analyses were performed to explore the functional roles of these genes. …”
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Effect of potato glycoside alkaloids on mitochondria energy metabolism of Fusarium solani, the root rot pathogen of Lycium barbarum by Ruiyun Li, Bin Wang, Wei Chen, Chongqing Zhang, Nan Li, Yupeng Wang, Yuke Yan, Yuyan Sun, Jing He, Jing He

“…Subsequent analysis focused on five DEPs related to energy metabolism for verification at both protein and gene levels. Gene Ontology (GO) function analysis revealed that the DEPs were primarily involved in the integral component of the membrane, intrinsic component of the membrane, pyridine-containing compound metabolic processes, carbon-oxygen lyase activity, and the endoplasmic reticulum, with a notable enrichment in membrane components. …”
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Identification and Immunological Characterization of Cuproptosis Related Genes in Preeclampsia Using Bioinformatics Analysis and Machine Learning by Tiantian Yu, Guiying Wang, Xia Xu, Jianying Yan

“…We identified 10 DECRGs conducted Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein–protein interaction (PPI) network. …”
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Insights from Dysregulated mRNA Expression Profile of β-Cells in Response to Proinflammatory Cytokines by Zhen Wang, Kunlin Huang, Jing Xu, Jia Liu, Ying Zheng

“…The results showed 809 upregulated and 946 downregulated protein-coding mRNAs in MIN6 cells upon the stimulation of cytokines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analyses were performed to predict the functions of dysregulated genes. …”
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Unravelling the transcriptomic symphony of muscle ageing: key pathways and hub genes altered by ageing and caloric restriction in rat muscle revealed by RNA sequencing by Gulam Altab, Brian J. Merry, Charles W. Beckett, Priyanka Raina, Inês Lopes, Katarzyna Goljanek-Whysall, João Pedro de Magalhães

“…RNA-seq data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. …”
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Identification of Differentially Expressed Genes and Signaling Pathways in Acute Myocardial Infarction Based on Integrated Bioinformatics Analysis by Da-Qiu Chen, Xiang-Sheng Kong, Xue-Bin Shen, Mao-Zhi Huang, Jian-Ping Zheng, Jing Sun, Shang-Hua Xu

“…These DEGs were performed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses by using Clusterprofiler package. …”
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Differential expressed genes (DEGs) and differential alternative splicing genes (DASs) revealed the common pathologic mechanism of three bacterial pathogens to American eels (Angui... by Zihao Chen, Guanghua Sun, Songlin Guo

“…Compared to the Con group, result of the RNA-seq of six infected groups showed 2247 common differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis identified 23 common terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted 18 common pathways. …”
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Proteome differences of dental stem cells between permanent and deciduous teeth by data-independent acquisition proteomics by Zhang Suping, Liu Yuqing, Dong Jin, Jiao Min, Gu Yongchun, Chen Liling, Yuan Na, Wang Jianrong, Yang Dezhao, Meng Fanwen

“…By comparing their expression levels, 209 differentially expressed proteins were identified. Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, along with protein–protein interaction network construction, revealed significant metabolic differences and key regulatory nodes. …”
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Clinical Value and Potential Mechanism of miRNA-33a-5p in Lung Squamous Cell Carcinoma by Xiang-Ming Wang, Shang-Wei Chen, Gang Chen, Hua-Fu Zhou, Ting-Qing Gan, Jing-Jing Zeng, Zu-Yun Li

“…The differentially expressed genes (DEGs) of LUSC and the candidate target genes of miRNA-33a-5p were overlapped to acquire a set of specific genes for further analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and protein–protein interaction (PPI) network. miRNA-33a-5p overexpressed in LUSC was supported by 706 LUSC and 261 non-LUSC samples gathering from RT-qPCR, miRNA-seq, and public miRNA microarrays. …”
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Mediating Mendelian randomization in the proteome identified potential drug targets for obesity-related allergic asthma by Jiannan Lin, Shuwen Lu, Xiaoyu Zhao

“…We further explored the functions and enriched pathways of the mediating proteins using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. …”
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WNT3A promotes the cementogenic differentiation of dental pulp stem cells through the FOXO1 signaling pathway by Dongmei Cheng, Yang Bao, Xue Wang, Haidong Xiang, Tianyuan Guo, Yong Du, Zhiyong Zhang, Han Guo

“…Pathway enrichment exploration was conducted utilizing gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Metascape tools. …”
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Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease by Daisuke Yoshihara, Masanori Kugita, Tamio Yamaguchi, Harold M. Aukema, Hiroki Kurahashi, Miwa Morita, Yoshiyuki Hiki, James P. Calvet, Darren P. Wallace, Takafumi Toyohara, Takaaki Abe, Shizuko Nagao

“…By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 downregulated gene ontology biological process gene sets and six of the top 20 curated gene set canonical pathways identified to be downregulated by PIOtreatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. …”
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Deciphering the multifaceted mechanism of Shuang Huang Lian in treating upper respiratory tract infections: A metabolomics-based network pharmacology approach by Gang Xu, Akshay Suresh Patil, Ruhan Wei, Dan Liu, Aimin Zhou, Yan Xu

“…A protein-protein interaction (PPI) network was constructed, and gene ontology (GO), KEGG, and Reactome enrichment analyses were conducted to elucidate the biological functions relevant to URTIs. …”
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Identification of candidate genes involved in Zika virus-induced reversible paralysis of mice by John D. Morrey, Venkatraman Siddharthan, Hong Wang, Alexandre L. R. Oliveira, Keiichiro Susuki, Rakesh Kaundal, Sara M. Freeman, Aaron J. Thomas, Naveen Duhan, Nathan G. Corry

“…To refine the search for candidate DEGs we used gene ontology analysis and RT-qPCR to select 3 DEGs that could be involved with the node of Ranvier function and 5 DEGs that could be involved with synaptic function. …”
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Genetic Mapping for Seed Aging Tolerance Under Multiple Environments in Sweet Corn by Yanchao Du, Jianting Lin, Haoxuan Jiang, Huating Zhao, Xuebiao Zhang, Ruigang Wang, Faqiang Feng

“…Candidate genes were explored within QTL cluster regions based on the aging-induced transcriptomic sequencing data of K62 and K107. Through Gene Ontology enrichment, gene annotation, and expression profiling clustering analyses, 12 positive candidate genes linked to seed aging tolerance were identified. …”
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Comprehensive Pan-Cancer Analysis and Functional Studies Reveal SLC2A6 as a Ferroptosis Modulator in Hepatocellular carcinoma by Guohong Yan, Hailian Huang, Ziyan Lu, Meifeng Chen, Xiang Wang, Pei Zhong, Chongjiu Qin, Shutian Mo, Chuangye Han, Xiaoling Luo, Xinping Ye

“…This study utilized multiple databases to investigate the relationship between SLC2A6 expression and clinical stage, methylation status, drug sensitivity, immune infiltration, and immune checkpoint regulation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. …”
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Identification and functional analysis of energy metabolism and pyroptosis-related genes in diabetic nephropathy by Shan He, Jian Ye, Yu Wang, Lu yang Xie, Si Yi Liu, Qin kai Chen

“…Subsequent analyses included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and Protein-Protein Interaction (PPI) network analysis. …”
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