Analysis of the circadian rhythm of biological processes in mouse liver and kidney by I. N. Podkolodnyy, N. N. Tverdokhleb, O. A. Podkolodnaya

“…A statistical analysis of enrichment of Gene Ontology terms in these twelve gene groups in the liver and kidneys was perform ed.  …”
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Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease by Yeonjeong Heo, Jeeyoung Kim, Seok-Ho Hong, Woo Jin Kim

“…Functional analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. …”
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Identification and mechanistic insights of cell senescence-related genes in psoriasis by Guiyan Deng, Cheng Xu, Dunchang Mo

“…Protein-protein interaction networks, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the functions and pathways of these genes. …”
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Ginsenoside Rh2 regulates triple-negative breast cancer proliferation and apoptosis via the IL-6/JAK2/STAT3 pathway by Rumeng Ding, Quancheng Kan, Ting Wang, Ran Xiao, Yanan Song, Duolu Li

“…Additionally, ELISA, Western blot, and quantitative real-time PCR were used to further investigate the mechanisms of ginsenoside Rh2-induced apoptosis in TNBC cells.ResultsThrough network analysis, 47 common targets were identified, and Gene Ontology (GO) enrichment analysis suggested that ginsenoside Rh2 may exert therapeutic effects in TNBC by influencing apoptosis, cell proliferation, and protein kinase activity. …”
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Regulation of reactive oxygen species and the role of mitochondrial apoptotic-related genes in rheumatoid arthritis by Conghui Gao, Chengqiang Zhang, Lixing Wen, Gailian Zhang, Xiaoping Liu, Jie Wang, Luping Cui, Rui Li, Tingting Nie, Jiaoniu Duan, Yingying Guo

“…Urgent exploration of RA-related mitochondrial apoptosis biomarkers is needed. Gene Expression Ontology (GEO)-derived RA datasets were used to identify differentially expressed genes (DEGs) compared to normal controls, intersected with MARGs to obtain differentially expressed mitochondrial apoptosis-related genes (DE-MARGs). …”
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Deciphering the Transcriptional Metabolic Profile of Adipose-Derived Stem Cells During Osteogenic Differentiation and Epigenetic Drug Treatment by Giulia Gerini, Alice Traversa, Fabrizio Cece, Matteo Cassandri, Paola Pontecorvi, Simona Camero, Giulia Nannini, Enrico Romano, Francesco Marampon, Mary Anna Venneri, Simona Ceccarelli, Antonio Angeloni, Amedeo Amedei, Cinzia Marchese, Francesca Megiorni

“…<i>In silico</i> annotation and gene ontology analysis highlighted the activation of ethanol oxidation, ROS regulation, retinoic acid metabolism, and steroid hormone metabolism, as well as in the metabolism of lipids, amino acids, and nucleotides, and pinpointed potential new osteogenic drivers like AOX1 and ADH1A. …”
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Overexpression of StBBX14 Enhances Cold Tolerance in Potato by Heng Zhang, Mingjun Chen, Xiaobo Luo, Li Song, Fei Li

“…A transcriptome analysis showed that a total of 2449 and 6274 differentially expressed genes were identified in WT-1 h and WT-12 h, respectively, when compared with WT-0h. A Gene Ontology enrichment analysis revealed that photosynthesis, cell wall, thylakoid, transcription regulator activity, oxidoreductase activity and glucosyltransferase activity were significantly enriched in <i>OE-StBBX14</i> and WT. …”
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Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins by Kazuma Yoshioka, Reiko Nakagawa, Chi Lieu Kim Nguyen, Hayate Suzuki, Kiyohiro Ishigaki, Seiya Mizuno, Tsukasa Okiyoneda, Shizufumi Ebihara, Kazuya Murata

“…Although there were no obvious differences in the interactome of USP46 between wildtype and ΔK92, a gene ontology analysis revealed that centrosome‐related proteins were significantly enriched in the proximal proteins of USP46. …”
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Inhibition of anti-tumour reactivity of immune cells in the salivary gland cancer: A proteomic approach by Rajdeep Chakraborty, Charbel Darido, Aidan Tay, Thiri Zaw, Shoba Ranganathan, Fei Liu, Giuseppe Palmisano

“…We performed SWATH, proteome profilers, gene ontology biological function, functional annotation clustering and protein interaction network analysis of all cancer samples in the co-culture models. …”
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Identification of Host–Protein Interaction Network of Canine Parvovirus Capsid Protein VP2 in F81 Cells by Hongzhuan Zhou, Huanhuan Zhang, Xia Su, Fuzhou Xu, Bing Xiao, Jin Zhang, Qi Qi, Lulu Lin, Kaidi Cui, Qinqin Li, Songping Li, Bing Yang

“…Subsequently, the protein Interaction Network (PPI), the annotation of gene ontology (GO) and the database of Kyoto Encyclopedia of Genes and Genomes (KEGG) were constructed for in-depth analysis. …”
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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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DHX37 Impacts Prognosis of Hepatocellular Carcinoma and Lung Adenocarcinoma through Immune Infiltration by Yanni Xu, Qiongchao Jiang, Hejun Liu, Xiaoyun Xiao, Dinghong Yang, Phei Er Saw, Baoming Luo

“…Coexpression genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and fundamental regulators were performed via LinkedOmics. …”
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Gene Expression Signatures of Peripheral Blood Mononuclear Cells during the Early Post-Transplant Period in Patients Developing Cardiac Allograft Vasculopathy by Khurram Shahzad, Martin Cadeiras, Sarfaraz Memon, Barry Zeeberg, Tod Klingler, Anshu Sinha, Esteban G. Tabak, Sreevalsa Unniachan, Mario C. Deng

“…We used significance analysis of microarrays to identify differentially expressed genes and High-Throughput GoMiner to assess gene ontology (GO) categories. We corroborated our findings by retrospective analysis of PBMC real-time PCR data from 33 patients. …”
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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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Clinical assessment and transcriptome analysis of host immune responses in a vaccination-challenge study using a glycoprotein G deletion mutant vaccine strain of infectious laryngo... by Gayathri Gopakumar, Mauricio J. C. Coppo, Mauricio J. C. Coppo, Andrés Diaz-Méndez, Carol A. Hartley, Joanne M. Devlin

“…Significant differences were observed in the tracheal transcriptome of the non-vaccinated-challenged birds compared to the other two groups. Enriched gene ontologies and pathways that indicated heightened immune responses and impairments to ciliary and neuronal functions, cell junction components, and potential damages to cartilaginous and extracellular components in the trachea of the non-vaccinated-challenged birds were consistent with their severe tracheal pathology compared to the other two groups. …”
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Compound exposure of 2.8 GHz and 9.3 GHz microwave causes learning and memory impairment in rats by Liu Sun, Xiaoya Wang, Ke Ren, Chuanfu Yao, Haoyu Wang, Xinping Xu, Hui Wang, Ji Dong, Jing Zhang, Binwei Yao, Xiaohui Wei, Ruiyun Peng, Li Zhao

“…However, both the cognitive function and hippocampal structure restored to normal at 28 d after exposure, which might be attributed to self-recovery mechanisms. Gene ontology (GO) and Protein-protein interaction (PPI) analyses of differential expressed genes (DEGs) in peripheral blood suggested that Htt and Bdnf might be potential indicators to predict microwave. …”
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Identification of blood transcriptome modules associated with suicidal ideation in patients with major depressive disorder by Min Wang, Hailin Xiang, Jinxue Wei, Yikai Dou, Yushun Yan, Yue Du, Huanhuan Fan, Liansheng Zhao, Rongjun Ni, Xiao Yang, Xiaohong Ma

“…An ANCOVA was conducted to assess differences in gene coexpression modules among groups, with age and sex included as covariates. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases were used to annotate module functions. …”
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An Integrated Approach Exploring the Synergistic Mechanism of Herbal Pairs in a Botanical Dietary Supplement: A Case Study of a Liver Protection Health Food by Liang Chen, Chun Hu, Molly Hood, Juntao Kan, Xiaona Gan, Xue Zhang, Yi Zhang, Jun Du

“…A total of sixteen chemical constituents of White Peony and Licorice were isolated and identified, which interact with 73 liver protection-related targets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed along with network analysis. …”
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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

“…Additionally, 1,210 differentially expressed genes were detected. 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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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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