Characterization and Study of Gene Expression Profiles of Human Periodontal Mesenchymal Stem Cells in Spheroid Cultures by Transcriptome Analysis by Takenori Suga, Michihiko Usui, Satoru Onizuka, Kotaro Sano, Tsuyoshi Sato, Kohji Nakazawa, Wataru Ariyoshi, Tatsuji Nishihara, Keisuke Nakashima

“…Transcriptome analysis was performed using spheroid and monolayer cultures of hPDLMSCs from four patients. Cluster and Gene Ontology analyses revealed that genes involved in cell-cell adhesion as well as the G2/M and G1/S transitions of mitotic cell cycles were strongly expressed in the monolayer culture group. …”
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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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Col1A1 as a new decoder of clinical features and immune microenvironment in ovarian cancer by Xiao Xiao, Fangyi Long, Shaolan Yu, Wengjuan Wu, Dayan Nie, Xiaoyan Ren, Wen Li, Xujuan Wang, Ling Yu, Pinghan Wang, Gang Wang

“…The LinkedOmics and INPUT2 databases were used to analyze differential gene expression in OC, This was followed by enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) annotations to identify and predict potential signaling pathways associated with COL1A1.ResultsOur study demonstrated that COL1A1 expression was significantly elevated in OC tissues compared to normal ovarian tissues. …”
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Genomic insights into genetic diversity and seed coat color change in common bean composite populations by Eva Plestenjak, Eva Plestenjak, Mohamed Neji, Lovro Sinkovič, Vladimir Meglič, Barbara Pipan

“…Cross-population statistics (XP-CLR and XP-EHH) were used to identify selection signals associated with seed coat color change. Gene Ontology (GO) and KEGG enrichment analyzes were performed for candidate genomic regions.ResultsPhenotypic analysis revealed significant differences in seed coat color among the four composite populations, with notable changes among years. …”
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Comparative Proteomic Analysis of Visceral Adipose Tissue in Morbidly Obese and Normal Weight Chinese Women by Chen Shang, Wei Sun, Chunlin Wang, Xiangqing Wang, Huijuan Zhu, Linjie Wang, Hongbo Yang, Xue Wang, Fengying Gong, Hui Pan

“…Differentially expressed VAT proteins were further analyzed with Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA). …”
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Spatially resolved transcriptomics reveals gene expression characteristics in uveal melanoma by Jing-Ying Xiu, Yu-Ning Chen, Ya-Li Mao, Jing-Ting Luo, Hao-Wen Li, Yang Li, Wen-Bin Wei

“…Methods In this paper, we performed spatial transcriptomics (ST) sequencing on two UM samples to describe the different cellular distribution patterns. Gene Ontology (GO) and Kyoto Encyclopedia of Genes, Genomes (KEGG) functional enrichment analysis, and protein–protein interaction (PPI) network were performed to define the biological function of each cluster. …”
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Transcriptome Analysis Reveals the Molecular Mechanism of PLIN1 in Goose Hierarchical and Pre-Hierarchical Follicle Granulosa Cells by Hua He, Yueyue Lin, Xi Zhang, Hengli Xie, Zhujun Wang, Shenqiang Hu, Liang Li, Hehe Liu, Chunchun Han, Lu Xia, Jiwei Hu, Jiwen Wang, Lin Liao, Xin Yuan

“…In this study, we used cell transfection technology combined with transcriptome sequencing to investigate the regulatory mechanism of <i>PLIN1</i> in goose follicular GCs. Gene Ontology (GO) analysis revealed that in the four groups (phGC: over_vs_over-NC; hGC: over_vs_over-NC; phGC: si_vs_si-NC; hGC: si_vs_si-NC), most differentially expressed genes (DEGs) were significantly enriched (<i>p</i> < 0.05) in pathways related to biological processes (BPs), particularly those associated with the regulation of cellular lipid metabolism and oxidative stress. …”
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Characteristics and multi-omics analysis of spontaneous spondyloarthritis in non-human primates: Case report by Lei Cai, Qing Lv, Ronghua Ma, Wei Liu, Yalun Guan, Zhongqiang Huang, Qingyu Liu, Yunfeng Li, Shuhua Liu, Ge Li, Yu Zhang

“…A total of eight genes and proteins with high expression levels were identified as common to both the transcriptome and proteome. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on these co-expressed genes and proteins, indicating a predominant enrichment in the IL-17 signaling pathway, with S100A8 and S100A9 identified as the core proteins. …”
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Integrative single-cell and bulk RNA-seq analyses identify CD4+ T-cell subpopulation infiltration and biomarkers of regulatory T cells involved in mediating the progression of athe... by Yifeng Zhang, Yifeng Zhang, Shuxian Lu, Shuxian Lu, Liang Qiu, Liang Qiu, Manman Qin, Manman Qin, Dan Shan, Lianhua Xie, Yao Yi, Yao Yi, Jun Yu

“…Subsequently, we identified significantly differential expressed genes of Tregs during the progression of atherosclerotic plaque and investigated the key pathways and transcription factors for these differentially expressed genes using gene ontology (GO) analysis and transcription factor enrichment analysis (TFEA), respectively. …”
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Exploration of the mechanism of Lithospermum erythrorhizon oil in treating atopic dermatitis based on network pharmacology and experimental validation of the PI3K-Akt pathway regul... by Weisheng Hu, Yinlan Wang, Yingjie Zhou, Junbao Shi, Zengyan Li, Xiaoling Jiang, Qinyuan Wu, Changming Zhong, Huilan Weng, Sijie Ouyang, Yuan Jing, Xianxiang Cai, Mingda Ye, Ning Huang

“…A protein-protein interaction (PPI) network was built using STRING, and functional analysis Gene Ontology (GO) and pathway enrichment Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on Metascape. …”
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Identification of positive selection signatures associated with milk and composition traits in Murciano-Granadina and Barki by Hossein Mohammadi, amir hossien khaltabadi farahani, Mohammad Hossein Moradi

“…Some of the genes under selection were found to be consistent with some previous studies|. Results of gene ontology analysis identified two biological pathways namely skeletal system development and calcium channel complex with two important KEGG pathways including glucagon signaling pathway and AMPK signaling pathway which play an important role in glucose metabolism and homeostasis and skeletal system development. …”
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Targeting NANOS1 in triple-negative breast cancer: synergistic effects of digoxin and PD-1 inhibitors in modulating the tumor immune microenvironment by Tangyi Wang, Yadian Lei, Jingwei Sun, Li Wang, Yuxin Lin, Zhijing Wu, Shoude Zhang, Chengzhu Cao, Chengzhu Cao, Chengzhu Cao, Haiyan Wang, Haiyan Wang, Haiyan Wang

“…RNA-seq analysis after target silencing by small interfering RNA (siRNA) was performed, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. …”
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Bulk and single-cell transcriptome revealed the metabolic heterogeneity in human glioma by Yong Xiao, Mengjie Zhao, Ran Wang, Liang Liu, Chong Xiang, Taiping Li, Chunfa Qian, Hong Xiao, Hongyi Liu, Yuanjie Zou, Xianglong Tang, Kun Yang

“…Kaplan–Meier analysis was conducted to compare clinical outcomes between different metabolic groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to elucidate the biological functions of genes of interest. …”
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红景天苷调控<italic>miRNA-1343-3p/MAP3K6/MMP24</italic>信号分子抑制胃癌细胞的增殖和侵袭 by 田雨, 王小平, 江锋, 曹晓岚, 侯鑫睿, 张振东

“…方法将人胃癌细胞（MGC-803）按照红景天苷药物浓度不同分为对照组（0 μmol/mL）和低（6 μmol/mL）中（12 μmol/mL）高（24 μmol/mL）红景天苷剂量组；CCK-8实验检测红景天苷药物对人胃癌细胞抗增殖作用；克隆形成实验检测红景天苷药物对人胃癌细胞克隆形成能力的影响；Transwell实验检测红景天苷对人胃癌细胞侵袭能力的影响；细胞划痕实验检测红景天苷对人胃癌细胞迁移能力的影响；高通量测序（RNA-seq）检测了胃癌细胞在红景天苷作用后24 h时对照组和药物组miRNA和mRNA的表达量，将具有明显差异表达的miRNA聚类并预测其靶基因。通过Gene Ontology（GO）和KEGG富集分析，预测差异表达miRNA靶基因的相关功能及相关代谢通路，并建立miRNA与靶基因mRNA间的互作网络。…”
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Intervention effect and mechanism of Dracocephalum moldavica L. extract on bleomycin-induced pulmonary fibrosis in rats by Xiaoyu SUN, Li CHEN, Ruifang GAO, Hui YU, Min JIN

“…The predicted potential targets were analyzed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses through the Database for Annotation, Visualization and Integrated Discovery (DAVID) and validated by molecular docking. …”
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Exploring the role of methylation-driven gene IFFO1 in pancreatic adenocarcinoma diagnosis, prognosis and cellular functions by XU Ziqi, HU Ruizhi, LI Junjian, WANG Hongxia, SANG Youzhou

“…Subsequently, differential analysis, gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) were performed. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…We utilised protein–protein interactions (PPIs), Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes to identify T2DM-associated MAFLD genes and potential mechanisms. …”
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Identification of reproductive performance in Bali-polled bulls using computer-assisted semen analysis and plasma seminal proteomics by Athhar Manabi Diansyah, Sanstoso Santoso, Herdis Herdis, Muhammad Yusuf, Tri Puji Priyatno, Tulus Maulana, Abdul Latief Toleng, Muhammad Ihsan Andi Dagong, Syahruddin Said, Hikmayani Iskandar, Aeni Nurlatifah, Puji Lestari, Lukman Affandy, Abdullah Baharun

“…Seminal plasma proteins were analyzed through liquid chromatography–tandem mass spectrometry (LC-MS/MS) and annotated using the UniProt database, PANTHER for gene ontology, and STRING database for protein interactions. …”
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Historical Analysis and Adaptation of the Issue of Good and Evil in Iranian, Ishraqi, and Sadrai Wisdom by Somayeh Karimi, Jafar Shanazari

“…This is complete proof of the historical course of the thought of good and evil in terms of ontology and epistemology from Iranian wisdom to Sadra. …”
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Weighted Gene Co-Expression Network of Growth Differentiation-Related lncRNAs and mRNAs in Plectropomus leopardus by Jin GAO, Jinye LIU, Fuxiao CHEN, Yongbo WANG, Shuyuan FU

“…The expression profiles of lncRNAs and mRNAs were acquired, and a Weighted Gene Co-expression Network Analysis (WGCNA) method was used to construct a co-expression network of growth differentiation related lncRNAs and mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes within specific gene modules were conducted to analyze the biological functions of the modules. …”
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