Correlation analysis of the impact of Clonorchis sinensis juvenile on gut microbiota and transcriptome in mice by Xueling Deng, Shitao Li, Yuhong Wu, Jiali Yao, Wei Hou, Jiangyao Zheng, Boying Liang, Xiaole Liang, Qiping Hu, Zhanshuai Wu, Zeli Tang

“…Gut transcriptome analysis demonstrated an increase in the number of differentially expressed genes (DEGs) as infection progressed. Enriched Gene Ontology items highlighted immune and detoxification-related processes, including immunoglobulin production and xenobiotic metabolic processes. …”
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Előszó by Kosztasz Rosta

“…Katona Ágnes a személyek konstitúciós elméletének kritikájára vállalkozik: tanulmányában arra mutat rá, hogy a „személyek ontológiájának” (personal ontology) vizsgálódási körén belül újabban népszerűvé vált konstitúciós nézet jelenlegi formájában inkonzisztens állításokat tartalmaz. …”
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Proteomics unveil candidate biomarkers and pathogenesis of subacute thyroiditis by Litong Ran, Xiufei Liu, Yongfeng Tian, Jiaran Zhu, Zhengyuan Gong, Qiao Qiao, Xin Jiang, Yuren Wang, Guojun Yang, Hongting Zheng, Yi Zheng, Hua Qu

“…Here, we profiled thyroid in situ protein alterations in fine-needle aspiration biopsy samples from SAT patients using proteomic analysis and uncovered 57 differentially abundant proteins. Gene ontology and KEGG enrichment analyses identified that these proteins were enriched in processes involving infection, inflammatory response and cell adhesion and junction, which likely contribute to the pathogenesis. …”
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Human Periodontal Ligament Stem Cell-Derived Exosomes Promote Bone Regeneration by Altering MicroRNA Profiles by Ting Liu, Wenyun Hu, Xue Zou, Jingchen Xu, Shushu He, Le Chang, Xinyi Li, Yuanyuan Yin, Mi Tian, Ziyu Li, Jialiang Zhou, Xiaoge Jiang, Song Chen

“…The results of Gene Ontology analysis and pathway analysis demonstrated that the target genes of differentially expressed exosomal miRNAs participate in the regulation of a variety of biological processes, such as catalytic activity, protein binding, metabolic processes, cell development, and differentiation, and are enriched in osteogenic differentiation-related pathways, such as MAPK signaling, AMPK signaling, and insulin signaling pathways. …”
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Investigation of metabolic features of glioblastoma tissue and the peritumoral environment using targeted metabolomics screening by LC-MS/MS and gene network analysis by N. V. Basov, A. V. Adamovskaya, A. D. Rogachev, E. V. Gaisler, P. S. Demenkov, T. V. Ivanisenko, A. S. Venzel, S. V. Mishinov, V. V. Stupak, S. V. Cheresiz, O. S. Oleshko, E. A. Butikova, A. E. Osechkova, Yu. S. Sotnikova, Y. V. Patrushev, A. S. Pozdnyakov, I. N. Lavrik, V. A. Ivanisenko, A. G. Pokrovsky

“…Analysis of the overrepresentation of Gene Ontology biological processes revealed the statistical significance of 184 processes, including apoptosis, the NF-kB signaling pathway, proliferation, migration, angiogenesis, and py­roptosis, many of which play an important role in oncogenesis. …”
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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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Single-cell profiling reveals a reduced epithelial defense system, decreased immune responses and the immune regulatory roles of different fibroblast subpopulations in chronic atro... by Lin Lin, Tingxuan Huang, Lizhi Li, Yang Lin, Feng Chen, Ziyi Zheng, Jie Zhou, Yizhe Wang, Weihao You, Yujie Duan, Yawen An, Shiwei He, Weimin Ye

“…The molecular changes were identified by comparing differentially expressed genes (DEGs) between the two mucosa states. Gene Ontology (GO) pathway enrichment analysis was used to explore the potential functional changes in each cell subtype in atrophic mucosa. …”
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Exploring the multi-targeted mechanism of Saikosaponin A in prostate cancer treatment: a network pharmacology and molecular docking approach by Genbao Zhu, Genbao Zhu, Genbao Zhu, Zhiming Jiang, Niuping Zhu, Niuping Zhu, Donghui Wang, Donghui Wang, Tianpeng Guo, Tianpeng Guo, Yiqing Meng, Yiqing Meng, Yi Zhu, Yi Zhu, Kemeng Tan, Mengxue Hu, Heng Tang, Xuannian Wang, Xuannian Wang

“…However, the mechanism underlying the effects of SSA in prostate cancer treatment remains elusive.MethodsIn this study, a network pharmacology approach was applied to identify relevant targets from drug- and disease-related databases, and intersections were analyzed using Venny2.1 to construct a Protein-Protein interaction (PPI) interaction network. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to elucidate associated biological functions and signaling pathways. …”
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Novel predictive biomarkers for atonic postpartum hemorrhage as explored by proteomics and metabolomics by Jiangxue Qu, Hai Jiang, Huifeng Shi, Nana Huang, Jiawen Su, Yan Zhang, Lian Chen, Yangyu Zhao

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) functional enrichment analysis of significantly differentially expressed proteins revealed that atonic PPH was associated with T cell- and macrophage-related immune inflammatory responses. …”
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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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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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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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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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