Mechanistic insights into pachymic acid’s action on triple-negative breast Cancer through TOP2A targeting by Ming Liu, Li Zheng, Yang Zhang, Jinhui Tian

“…Enrichment analysis included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). …”
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The impaired response of nasal epithelial cells to microplastic stimulation in asthma and COPD by Magdalena Paplińska-Goryca, Paulina Misiukiewicz-Stępień, Monika Wróbel, Katarzyna Mycroft-Rzeszotarska, Dorota Adamska, Julia Rachowka, Milena Królikowska, Krzysztof Goryca, Rafał Krenke

“…Microplastic exposure induced inflammatory cytokine secretion only for IL-8 production in controls (epithelial/ moMφs co-culture) and asthmatic (monoculture) epithelial cells in contrast to PM2.5, which was a strong inflammatory inducer. Gene Ontology analysis revealed that microplastic exposure affected sterol and cholesterol biosynthesis, secondary alcohol metabolism, and acetyl-CoA metabolism in asthma, and cell motility, chemokine signaling, leukocyte migration, and chemotaxis in COPD. …”
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Orthoweb: a software package for evolutionary analysis of gene networks by R. A. Ivanov, A. M. Mukhin, F. V. Kazantsev, Z. S. Mustafin, D. A. Afonnikov, Y. G. Matushkin, S. A. Lashin

“…Orthoweb also includes optional analytical features, such as the ability to explore Gene Ontology (GO) terms associated with genes, facilitating functional enrichment analyses that link evolutionary origins of genes to biological processes. …”
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Expression and prognostic value of ferritinophagy-related NCOA4 gene in low-grade glioma: integration of bioinformatics and experimental validation by Guangtang Chen, Xueping Shi, Rukai Jiao, Jiacai Qian, Xiaolin Du, Jian Liu, Xi Zeng

“…Multivariate Cox regression identified NCOA4, age, CD8 T cells, and macrophages as LGG independent prognostic factors (all p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that NCOA4’s primary function in LGG is related to autophagy processes (all p < 0.05). …”
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Multitarget Effects of Danqi Pill on Global Gene Expression Changes in Myocardial Ischemia by Qiyan Wang, Hui Meng, Qian Zhang, Tianjiao Shi, Xuefeng Zhang, Mingyan Shao, Linghui Lu, Jing Wang, Wei Wang, Chun Li, Yong Wang

“…Differentially expressed genes among the sham group, model group, and DQP group were analyzed. The gene ontology enrichment analysis and pathway analysis of differentially expressed genes were carried out. …”
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Synovial Macrophages in Rheumatoid Arthritis: The Past, Present, and Future by Jiajie Tu, Xinming Wang, Xun Gong, Wenming Hong, Dafei Han, Yilong Fang, Yawei Guo, Wei Wei

“…However, no systematic analysis to identify SM ontology in either physiological or pathological conditions has been available to date. …”
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Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning by Wei Chen, Zeyan Xu, Haitao Sun, Wen Feng, Zhenhua Huang

“…Differentially expressed ubiquitination-related genes were identified by intersecting differentially expressed genes (DEGs) from the GSE95095 dataset in the Gene Expression Omnibus (GEO) database with a set of ubiquitination-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. …”
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Key wound healing genes as diagnostic biomarkers and therapeutic targets in uterine corpus endometrial carcinoma: an integrated in silico and in vitro study by Fuchuan Jiang, Sajjad Ahmad, Sadia kanwal, Yasir Hameed, Qian Tang

“…Results Seventy wound healing-associated genes were extracted from the Gene Ontology (GO) database, and a protein-protein interaction (PPI) network was constructed using the STRING database. …”
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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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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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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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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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