A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy by Qing Tang, Ying Xu, Canhui Deng, Chaohua Cheng, Zhigang Dai, Zemao Yang, Chan Liu, Jianguang Su

“…Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to “cell differentiation” and “cell cycle process,” as significant factors regulating apomeiosis. …”
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IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis by Qi Wang, Xufeng Huang, Shujing Zhou, Yuntao Ding, Huizhi Wang, Weiye Jiang, Min Xu

“…Based on the enrichment results of the “Gene Ontology“(GO) and “Kyoto Encyclopedia of Genes and genomes “(KEGG) as well as documented findings of key genes, we further emphasized the potential of IL1RN and PRRX1 as markers of immune infiltrates in CRC and confirmed our hypothesis by compiling data from the UALCAN, Tumor Immune Estimation Resource, and TISIDB databases for these two genes. …”
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Construction of an lncRNA-mediated ceRNA network to investigate the inflammatory regulatory mechanisms of ischemic stroke. by Meimei Xu, Shan Yuan, Xing Luo, Mengsi Xu, Guangze Hu, Zhe He, Xinyuan Yang, Rui Gao

“…This led to the establishment of a comprehensive lncRNA-miRNA-mRNA regulatory network comprising 12 lncRNAs, 16 sponge miRNAs, and 191 target mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that differentially expressed mRNAs (DEmRNAs) were significantly enriched in stroke-related pathways. …”
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Bioinformatics Analysis of Genes and Mechanisms in Postherpetic Neuralgia by Yong Qiu, Meng-Lei Hao, Xu-Tao Cheng, Zhen Hua

“…Differentially expressed genes (DEGs) were identified and analyzed by Gene Ontology. Protein-protein interaction (PPI) network was constructed. …”
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Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer by Qin Bian, Haijun Li, Xiaoyi Wang, Tingting Liang, Kai Zhang

“…Then, overlapped differentially expressed genes (DEGs) between T2D verse control and SLC24A2-high verse SLC24A2-low were extracted and imported into weighted correlation network analysis. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis were used for functional enrichment analysis of DEGs. …”
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Identification of retinol dehydrogenase 10 as a shared biomarker for metabolic dysfunction-associated steatotic liver disease and type 2 diabetes mellitus by Fangyu Li, Rui Li, Hongjun Deng

“…We also analyzed the enriched pathways of shared genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. …”
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Identification of Iron Homeostasis Genes Dysregulation Potentially Involved in Retinopathy of Prematurity Pathogenicity by Microarray Analysis by Xian-qiong Luo, Chun-yi Zhang, Jia-wen Zhang, Jing-bo Jiang, Ai-hua Yin, Li Guo, Chuan Nie, Xu-zai Lu, Hua Deng, Liang Zhang

“…The one-class algorithm in significance analysis of microarray (SAM) software was used to screen the differentially expressed genes (DEGs) and quantitative RT-PCR (qRT-PCR) was conducted to validate the results. Gene Ontology was employed for functional enrichment analysis. …”
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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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The Intersection of Quranic Studies and Modern Technology: A Bibliometric Analysis of Academic Publications from 2000 to 2024 by Andri Nirwana AN, Mahmudulhassan Mahmudulhassan, Mohamad Ali, Muthoifin Muthoifin, Waston Waston, Abdul Rahman Bin S. Senathirajah

“…Important phrases like “Quran,” "ontology,” and “engineering education” became crucial to narrowly targeted study projects. …”
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Differences in gene expression profile between vocal cord Leukoplakia and normal larynx mucosa by gene chip by Jianhua Peng, He Li, Jun Chen, Xianming Wu, Tao Jiang, Xiaoyun Chen

“…In this study, we used microarrays to investigate the aberrantly expressed lncRNAs and mRNAs in vocal cord leukoplakia and adjacent non-neoplastic tissues. Methods Gene Ontology and pathway analyses were performed to determine the significant function and pathways of the differentially expressed mRNAs. qRT-PCR was performed to further validate the expression of selected lncRNAs and mRNAs in vocal cord leukoplakia. …”
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A Network-Based Approach to Explore the Mechanism and Bioactive Compounds of Erzhi Pill against Metabolic Dysfunction-Associated Fatty Liver Disease by Shaojie Huang, Fei Mu, Fei Li, Wenjun Wang, Haixia Chen, Lu Lei, Yang Ma, Yi Ding, Jingwen Wang

“…This was carried out through target prediction, protein-protein interaction (PPI) network construction, gene ontology, KEGG pathway enrichment, and molecular docking. …”
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Transcriptomics reveals substance biosynthesis and transport on membranes of Listeria monocytogenes affected by antimicrobial lipopeptide brevilaterin B by Yangliu Liu, Yawei Ning, Zhou Chen, Panpan Han, Tongxin Zhi, Siting Li, Aijin Ma, Yingmin Jia

“…Transcriptomic analysis showed 1779 difference expressed genes, including 895 up-regulated and 884 down-regulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that brevilaterin B influenced multiple pathways of L. monocytogenes, including peptidoglycan biosynthesis, membrane transport (ATP-binding cassette transports, ion transport), cellular metabolism (amino acid and lipid metabolism), ATP synthesis, and activation of the stress response (quorum sensing and bacterial chemotaxis). …”
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Elevated LIF and JAK-STAT activation drive severe COVID-19 in myeloma patients receiving the BCMA-CD3 bispecific antibody Elranatamab by Ziping Li, Fujing Zhang, Xianghong Jin, Junling Zhuang

“…Principal component analysis and clustering showed distinct protein expression profiles between the BiTe and PI groups. Gene Ontology (GO) analysis revealed that DEPs between the BiTe and PI groups were related to cytokine activity and leukocyte migration. …”
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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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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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Integrative single-cell and multi-omics analyses reveal ferroptosis-associated gene expression and immune microenvironment heterogeneity in gastric cancer by Shupeng Zhang, Zhaojin Li, Gang Hu, Hekai Chen

“…Subsequent analyses, including gene set intersection and functional enrichment, pinpointed genes implicated in ferroptosis and conducted comprehensive Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to elucidate their biological roles. …”
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circRNA Expression Profile in Dental Pulp Stem Cells during Odontogenic Differentiation by Ming Chen, Yeqing Yang, Junkai Zeng, Zilong Deng, Buling Wu

“…Based on microarray data from this study and available in the database, a ceRNA network was constructed to investigate the potential function of circRNAs during odontogenesis. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential correlation between signaling pathways and circRNAs. …”
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Prioritization of genes associated with the pathogenesis of leukosis in cattle by N. S. Yudin, N. L. Podkolodnyy, T. A. Agarkova, E. V. Ignatieva

“…The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. …”
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Exploring molecular disparities of H-type vasculature endothelial cells in osteonecrosis of the femoral head through single-cell analysis by Wei Shi, Dong Li, Qian Xu, Kai Zhang, Xinyu Liang, Hui Li, Zhijun Li, Huafeng Zhang

“…Molecular differences were assessed using Gene Ontology and KEGG analysis. Hypoxia, ferroptosis, pyroptosis, and parthanatos indices were calculated, and transcription factors were predicted using SENIC. …”
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