Improved Predictability of Diagnosis and Prognosis Using Serum‐ and Tissue‐Derived Extracellular Vesicles From Bulk mRNA Sequencing in Pancreatic Ductal Adenocarcinoma by Qian Zhu, Zhang Chen, Ming Tian, Xin Yan, Xiangdong Gongye, Zhicheng Liu, Anbang Zhao, Zhiyong Yang, Yufeng Yuan

“…Results The combination of miR142‐3p, miR148a‐3p, and CA199 showed a higher AUC (0.747) compared to CA199 alone (0.716) in ROC curve analysis. Gene Ontology (GO) annotations revealed that the two‐miRNA panel was associated with multiple oncogenic pathways. …”
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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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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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TMEM147 Correlates with Immune Infiltration and Serve as a Potential Prognostic Biomarker in Hepatocellular Carcinoma by Sheng Cheng, Jutang Li, Ming Xu, Qun Bao, Jiaoxiang Wu, Peng Sun, Bo Han

“…The functions of the TMEM147-related differentially expressed genes (DEGs) were identified by Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and gene set enrichment analysis (GSEA). …”
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Ascertaining provider-level implicit bias in electronic health records with rules-based natural language processing: A pilot study in the case of prostate cancer. by Ashwin Ramaswamy, Michael Hung, Joe Pelt, Parsa Iranmahboub, Lina P Calderon, Ian S Scherr, Gerald Wang, David Green, Neal Patel, Timothy D McClure, Christopher Barbieri, Jim C Hu, Charlotta Lindvall, Douglas S Scherr

“…Natural language processing screened human annotation using validated regex ontologies evaluated each provider's care on four prostate cancer quality indicators: (1) active surveillance utilization; (2) molecular biomarker discussion; (3) urinary function evaluation; and (4) sexual function evaluation. …”
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Effects of Baicalin on Gout Based on Network Pharmacology, Molecular Docking, and in vitro Experiments by Liu C, Liu W, Lu H, Fan Y, Wang A

“…Then, the potential targets and signaling pathways were acquired via protein–protein interaction (PPI), as well as the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. …”
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A graph neural network approach for hierarchical mapping of breast cancer protein communities by Xiao Zhang, Qian Liu

“…Results Using a large amount of publicly available proteomics data, we created a hierarchical tree for breast cancer protein communities using a novel hierarchical graph neural network, with the supervision of gene ontology terms and assistance of a pre-trained deep contextual language model. …”
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Anti-lung Cancer Mechanism of Quercetin Based on Network Pharmacology and Experimental Validation by Yi WANG, Xiaofang PU

“…Target enrichment analysis was carried out using the DAVID database, along with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. …”
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Potential Biomarkers for Predicting the Risk of Developing Into Long COVID After COVID‐19 Infection by Zhiyong Hou, Yu Ming, Jun Liu, Zhong Wang

“…The integration of both DEGs and differentially expressed module‐genes (DEMGs) regarding long COVID and COVID‐19 was intersected by following Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). …”
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Mechanisms of breast cancer treatment using Gentiana robusta: evidence from comprehensive bioinformatics investigation by Bo Xiong, Xinxin Zhang, Dongzhi Sangji, Lianghong Ni, Mingjie Fan, Beibei Fan

“…Building upon prior research on QJ’s chemical constituents, we conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using the DAVID database. …”
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Crucial Genes in Aortic Dissection Identified by Weighted Gene Coexpression Network Analysis by Hongliang Zhang, Tingting Chen, Yunyan Zhang, Jiangbo Lin, Wenjun Zhao, Yangyang Shi, Huichong Lau, Yang Zhang, Minjun Yang, Cheng Xu, Lijiang Tang, Baohui Xu, Jianjun Jiang, Xiaofeng Chen

“…The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was also utilized to analyze Gene Ontology (GO). Results. DEG analysis revealed that 1,113 genes were associated with AD. …”
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Identification of biomarkers associated with coronary artery disease and non-alcoholic fatty liver disease by bioinformatics analysis and machine learning by Chuan Lu, Mei Han, Qiqi Ma, Li Ying, Yue Zhang

“…A total of 554 overlapping DEGs associated with CAD and NAFLD were obtained by analysis of GSE113079 and GSE89632 datasets. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that the co-DEGs were significantly enriched in immune effector process, inflammation response and lipid metabolism. …”
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The functional insight into the genetics of cardiovascular disease: results from the post-GWAS study by L. O. Bryzgalov, E. E. Korbolina, I. S. Damarov, T. I. Merkulova

“…A significant impact on binding sites of thirteen TFs including those involved in blood cells formation, hematopoiesis, macrophage function, inflammation, and vasoconstriction was found in K562 cells. 21 rSNP gene targets and 5 partners predicted by PPI were enriched for spliceosome and endocytosis KEGG pathways, endosome sorting complex and mRNA splicing REACTOME pathways. Related Gene Ontology terms included mRNA splicing and processing, endosome transport and protein catabolic processes. …”
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MicroRNA-Based Markers of Oral Tongue Squamous Cell Carcinoma and Buccal Squamous Cell Carcinoma: A Systems Biology Approach by Setareh Shojaei, Pouya Menbari, Shokoofeh Jamshidi, Amir Taherkhani

“…Thus, we aimed to indicate signaling pathways, Gene Ontology terms, and prognostic markers mediating the malignant transformation of the normal oral tissue to OTSCC and BSCC. …”
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Active Ingredients and Potential Mechanism of Additive Sishen Decoction in Treating Rheumatoid Arthritis with Network Pharmacology and Molecular Dynamics Simulation and Experimenta... by Ren J, Liu Z, Qi X, Meng X, Guo L, Yu Y, Dong T, Li Q

“…Additive Sishen decoction (ASSD) is a widely used traditional Chinese medicine for the treatment of RA; however, its active ingredients and the mechanism of its therapeutic effects remain unclear.Methods: To predict the ingredients and key targets of ASSD, we constructed “drug-ingredient-target-disease” and protein–protein interaction networks. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the potential mechanism. …”
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Integrative Bioinformatics Analysis Unravel the Association between Intracerebral Hemorrhage and Cellular Apoptosis through Immune Infiltration by Pandi Chen, Gengfan Ye, Jia Li, Kuan Feng, Guangyao Zhu, Maosong Chen, Wei Chen

“…We retrieved microarray data of ICH patients from the Gene Expression Omnibus database and intersected it with apoptotic genes, filtering out apoptosis-related differentially expressed genes (ARDEGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted, and a logic regression-based diagnostic model for ICH was constructed. …”
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Textbooks on the international relations theory: What they talk about, what they keep silent about, and what to do about it by N. V. Yudin

“…The latter imply reliance on extremely shaky philosophical assumptions, which, consciously or not, reproduce post-modernist views on the problems of ontology and epistemology of international relations and international studies. …”
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