Essential oils from Amorpha fruticosa against hepatocellular carcinoma based on network pharmacology by Yixian Liu, Xiaojun Zhang, Jiacong Hao, Ying Zhao, Min Zou, Huiping Chen, Jintao Zhang

“…Then a PPI network, compound-target network, compound-target-pathway network, gene ontology, and KEGG enrichment for HCC were applied to identify the targets and pathways for AFLEO and AFFEO against HCC. …”
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Next generation sequencing uncovers multiple miRNAs associated molecular targets in gallbladder cancer patients by Rahul Saxena, Baskar Chakrapani, M. P. Sarath Krishnan, Amit Gupta, Sweety Gupta, Jayanta Das, Subash C. Gupta, Anissa A. Mirza, Shalinee Rao, Bela Goyal

“…Biological processes and related pathways were determined using the Panther and Gene Ontology databases. 439 significantly differentially expressed miRNAs were identified; 19 of them were upregulated and 29 were downregulated. …”
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Integrated bioinformatics and experimental analysis of CHAF1B as a novel biomarker and immunotherapy target in LUAD by Wei Du, Xiao-Wei Wu, Qing-Feng Li, Bing-Yu Zhang, Jing Wu, Ya-Ping Xu, Xue Yi

“…Using The Cancer Genome Atlas (TCGA) LUAD database, we analyzed the diagnostic and prognostic significance of CHAF1B and its association with immune infiltration and immunological checkpoints. Gene ontology (GO) enrichment and single-cell function analyses were employed to investigate CHAF1B's possible biological roles. …”
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Difference in the Vitreal Protein Profiles of Patients with Proliferative Diabetic Retinopathy with and without Intravitreal Conbercept Injection by Chen Zou, Minjie Zhao, Jingjing Yu, Dandan Zhu, Yunzhi Wang, Xinping She, Yanan Hu, Zhi Zheng

“…Liquid chromatography-tandem mass spectrometry- (LC-MS/MS-) based proteomic methods were used to determine the protein profiles of the vitreous humor in patients with PDR treated with (IVC group; n=9) and without (PDR group; n=8) preoperative IVC. Gene ontology (GO) annotation and REACTOME pathway analysis were obtained to overview differentially expressed proteins between each group. …”
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Characterizing the pan-cancer role of exosomal miRNAs in metastasis across cancers by Piyush Agrawal, Gulden Olgun, Arashdeep Singh, Vishaka Gopalan, Sridhar Hannenhalli

“…We observed significantly higher GC content in exomiRs relative to genomic background. Gene Ontology analysis revealed both general cancer processes, such as wound healing and epithelial cell proliferation, as well as cancer-specific processes, such as “angiogenesis” in the kidney and “ossification” in the lung. …”
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Identification of the Key Genes and Pathways in Esophageal Carcinoma by Peng Su, Shiwang Wen, Yuefeng Zhang, Yong Li, Yanzhao Xu, Yonggang Zhu, Huilai Lv, Fan Zhang, Mingbo Wang, Ziqiang Tian

“…Differentially expressed genes (DEGs) were screened by bioinformatics analysis. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction were performed to obtain the biological roles of DEGs in EC. …”
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Generation and analysis of mouse embryonic stem cells with knockout of the <i>Mcph1</i> (microcephalin) gene by A. M. Yunusova, A. V. Smirnov, T. A. Shnaider, I. E. Pristyazhnuk, S. Y. Korableva, N. R. Battulin

“…In this study, we generated several mouse embryonic stem cell (mESC) lines with knockout of the Mcph1 gene and analyzed their gene expression profile. Gene Ontology analyses of differentially expressed genes (DEGs) after Mcph1 knockout revealed gene categories related to general metabolism and olfactory receptor function but not to cell cycle control previously described for Mcph1. …”
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Screening and Whole-Genome Sequencing Analysis of Fructofuranose-Metabolizing Lactiplantibacillus plantarum 19M03 by SUN Daqing, QI He, DI Ziqing, GE Xianglin, HONG Qingping, DU Xinrui, YAO Yuxi, LI Hongfei

“…The results of gene function annotation showed that its genome sequence contained a total of 357 genes encoding carbohydrate-active enzymes (CAZymes) and 351 genes encoding carbohydrate transport proteins in the Clusters of Orthologous Groups of proteins (COGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and CAZy databases, as well as 12 genes related to fructan metabolism and transport, respectively. …”
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Orientin Reduces the Effects of Repeated Procedural Neonatal Pain in Adulthood: Network Pharmacology Analysis, Molecular Docking Analysis, and Experimental Validation by Dong-Dong Guo, Hai-Yan Huang, Hai-E. Liu, Kun Liu, Xing-Jing Luo

“…A protein-protein interaction (PPI) network was constructed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential mechanism of action. …”
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Identification and Verification of Hub Mitochondrial Dysfunction Genes in Osteoarthritis Based on Bioinformatics Analysis by Hui Niu, Xingxing Deng, Qian Zhang, Yijun Zhao, Jinfeng Wen, Wenyu Li, Huan Liu, Xiong Guo, Cuiyan Wu

“…The differentially expressed mitochondrial dysfunction genes (DEMDFGs) between OA and control samples were screened. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes pathways were analyzed for DEMDFGs. …”
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ORGANICITY OF THE PHENOMENON OF CULTURE AS AN EXPLICATION OF VITALITY by D. B. Svyrydenko, O. D. Yatsenko, O. V. Prudnikova

“…The position of authors position consists in the need to understand culture as an environmentally appropriate and dimensional phenomenon, the content and strategies of which are determined by a single ontology. Conclusions. The analysis let authors understand the voluntarily chaotic element of life. …”
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The storage quality and transcriptome analysis of fresh-cut taro by L-ascorbic acid combined with ultrasonic treatment by Lin Chen, Bingzhi Chen, Lulu Chu, Lili Chen, Luyu Xie, Youjin Deng, Yuji Jiang

“…Transcriptome analysis revealed that differentially expressed genes (DEGs) between the AS and CK groups were annotated and categorized into 50 and 20 functional groups based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. …”
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Myeloid dendritic cells and periodontal disease association: integrated study of single-cell sequencing and Mendelian randomization analysis by ChengJi Shi, XinYi Ou, XiaoXu Lei, LiJuan Huang, ShuHao Xu, Wei Li, Xi Zhao

“…MR analysis identified twenty-six significant genes, with LIMA1 (LIM domain and actin-binding 1) demonstrating a robust causal association with the progression of periodontal disease. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses highlighted crucial pathways involved in periodontal inflammation and tissue destruction. …”
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RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension by Yifan Wang, Guanyin Zhu, Fang Pei, Yigan Wang, Jun Liu, Caixia Lu, Zhihe Zhao

“…We used RNA-seq to identify differentially expressed miRNAs in periodontal tissues of the treatment group and control group tree shrews. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for enrichment analysis. …”
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Comprehensive bioinformatics analysis identifies metabolic and immune-related diagnostic biomarkers shared between diabetes and COPD using multi-omics and machine learning by Qianqian Liang, Yide Wang, Zheng Li, Zheng Li, Zheng Li, Zheng Li

“…Through cross-analysis, we identified the shared DEGs of COPD and diabetes, and investigated alterations of signaling pathways using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA). …”
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Insights of cellular and molecular changes in sugarcane response to oxidative signaling by Lucas Felipe Silva, Kellya F. M. Barreto, Helaine Cristiane Silva, Iara Dantas de Souza, Carlos H. S. G. Meneses, Adriana F. Uchôa, Katia C. Scortecci

“…Functional annotation through Gene Ontology and KEGG pathway enrichment showed that oxidative signaling led to the repression of photosynthesis-related pathways in leaves, while promoting pathways related to protein processing, glycolysis, and carbon metabolism in roots. …”
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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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