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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Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study by Ahmad Golestanifar, Hengameh Khedri, Parisa Noorabadi, Mohammadreza Saberiyan

“…Our approach combined differential expression analysis, functional enrichment through Gene Ontology (GO) and KEGG pathway mapping, and a Protein-Protein Interaction (PPI) network to identify crucial hub genes in KIRC progression. …”
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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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Differential Gene Expression Analysis in a Lumbar Spinal Stenosis Rat Model via RNA Sequencing: Identification of Key Molecular Pathways and Therapeutic Insights by Jin Young Hong, Wan-Jin Jeon, Hyunseong Kim, Changhwan Yeo, Hyun Kim, Yoon Jae Lee, In-Hyuk Ha

“…Functional enrichment analysis revealed that these DEGs included those involved in key biological processes, including synaptic plasticity, extracellular matrix organization, and hormonal regulation. Gene ontology analysis highlighted critical molecular functions such as mRNA binding and integrin binding, as well as cellular components such as contractile fibers and the extracellular matrix, which were significantly affected by LSS. …”
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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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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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The Identification of Key Genes and Pathways in Glioma by Bioinformatics Analysis by Mingfa Liu, Zhennan Xu, Zepeng Du, Bingli Wu, Tao Jin, Ke Xu, Liyan Xu, Enmin Li, Haixiong Xu

“…The glioma gene expression profile GSE4290 was analyzed for differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied for the enriched pathways. …”
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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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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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Transcriptomics and Physiological Analyses of Soybean Stay-Green Syndrome by Dagang Wang, Yanan Wang, Ruidong Sun, Yong Yang, Wei Zhao, Guoyi Yu, Yueying Wang, Feng Wang, Lin Zhou, Zhiping Huang

“…DEGs were classified using gene ontology (GO) terms, and photosynthesis-related genes <i>α-glucosidase</i>, <i>β-mannosidase</i>, <i>β-amylase 5</i> (<i>GmBAM5</i>), and <i>starch synthase 2</i> (<i>GmSS2</i>) were up-regulated. …”
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Proximity Labeling-Based Identification of MGAT3 Substrates and Revelation of the Tumor-Suppressive Role of Bisecting GlcNAc in Breast Cancer via GLA Degradation by Bowen Wang, Xin He, Yue Zhou, Zengqi Tan, Xiang Li, Feng Guan, Lei Lei

“…This approach enriched 116 and 189 proteins, respectively, identifying 17 common substrates shared with bisecting GlcNAc-bearing proteome obtained via intact glycopeptide enrichment methods. Gene ontology analysis revealed that the enriched proteins were predominantly localized in the exosome, endoplasmic reticulum, and Golgi apparatus, consistent with subcellular localization of MGAT3 substrates. …”
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Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds by N. S. Yudin, D. M. Larkin

“…Among them, the most promising for further research are the ASPH, NCKAP5L, SERPINF1, and SND1 genes. Gene ontology analysis indicated the existence of possible common biochemical path-ways for adaptation to cold in domestic and wild mammals associated with cytoskeleton disassembly and apoptosis.…”
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Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.) by Eun Soo Seong, Ji Hye Yoo, Jae Hoo Choi, Chang Heum Kim, Mi Ran Jeon, Byeong Ju Kang, Jae Geun Lee, Seon Kang Choi, Bimal Kumar Ghimire, Chang Yeon Yu

“…Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. …”
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Combination of inflammatory proteins in serum can be used to diagnose papillary thyroid carcinoma with lymph node metastasis by Yongqin Pan, Guanghao Wang, Delin Chen, Zhihui Wu, Yimwing Kei, Mingxi Xu

“…Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic validity. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis were used to analyze the potential regulatory pathways. …”
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Macrophages Phenotype Regulated by IL-6 Are Associated with the Prognosis of Platinum-Resistant Serous Ovarian Cancer: Integrated Analysis of Clinical Trial and Omics by Xiaoqing Wu, Wenping Lu, Chaojie Xu, Cuihong Jiang, Zhili Zhuo, Ruipeng Wang, Dongni Zhang, Yongjia Cui, Lei Chang, Xi Zuo, Ya’nan Wang, Heting Mei, Weixuan Zhang, Mengfan Zhang, Chen Li

“…The differential expression genes (DEGs) were analyzed via protein–protein interaction network, Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis to reveal major pathways of DEGs. …”
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A practical approach to building a calcareous nannofossil knowledge graph by Hongyi Zhao, Bin Hu, Chao Ma, Shijun Jiang, Yi Zhang, Xin Li, Lirong Chen, Can Cai, Longgang Ye, Shengjian Zhou, Chengshan Wang

“…By delving into the structured data associated with calcareous nannofossil biozones (the UC zone, CC zone and NC zone), we propose an ontology to describe the semantic units and logical relationships of paleontological biozones and species and then integrate relevant species records from unstructured research reports to construct a knowledge graph for calcareous nannofossils, that integrates multisource paleobiological data and knowledge reconstruction. …”
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