Effect of potato glycoside alkaloids on mitochondria energy metabolism of Fusarium solani, the root rot pathogen of Lycium barbarum by Ruiyun Li, Bin Wang, Wei Chen, Chongqing Zhang, Nan Li, Yupeng Wang, Yuke Yan, Yuyan Sun, Jing He, Jing He

“…Subsequent analysis focused on five DEPs related to energy metabolism for verification at both protein and gene levels. Gene Ontology (GO) function analysis revealed that the DEPs were primarily involved in the integral component of the membrane, intrinsic component of the membrane, pyridine-containing compound metabolic processes, carbon-oxygen lyase activity, and the endoplasmic reticulum, with a notable enrichment in membrane components. …”
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Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation by Imelda Ontoria-Oviedo, Itziar Palacios, Joaquín Panadero, Belén Sánchez, Francisco García-García, Adolfo López-Cerdán, Akaitz Dorronsoro, Delia Castellano, Luis Rodríguez-Borlado, Antonio Bernad, Pilar Sepúlveda

“…Analysis of the receptome of CPCs and BM-MSCs showed that gene ontology biological processes and KEGG pathways associated with adhesion mechanisms were upregulated in CPCs compared with BM-MSCs. …”
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Identification and Immunological Characterization of Cuproptosis Related Genes in Preeclampsia Using Bioinformatics Analysis and Machine Learning by Tiantian Yu, Guiying Wang, Xia Xu, Jianying Yan

“…We identified 10 DECRGs conducted Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein–protein interaction (PPI) network. …”
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Insights from Dysregulated mRNA Expression Profile of β-Cells in Response to Proinflammatory Cytokines by Zhen Wang, Kunlin Huang, Jing Xu, Jia Liu, Ying Zheng

“…The results showed 809 upregulated and 946 downregulated protein-coding mRNAs in MIN6 cells upon the stimulation of cytokines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analyses were performed to predict the functions of dysregulated genes. …”
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Unravelling the transcriptomic symphony of muscle ageing: key pathways and hub genes altered by ageing and caloric restriction in rat muscle revealed by RNA sequencing by Gulam Altab, Brian J. Merry, Charles W. Beckett, Priyanka Raina, Inês Lopes, Katarzyna Goljanek-Whysall, João Pedro de Magalhães

“…RNA-seq data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. …”
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Identification of Differentially Expressed Genes and Signaling Pathways in Acute Myocardial Infarction Based on Integrated Bioinformatics Analysis by Da-Qiu Chen, Xiang-Sheng Kong, Xue-Bin Shen, Mao-Zhi Huang, Jian-Ping Zheng, Jing Sun, Shang-Hua Xu

“…These DEGs were performed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses by using Clusterprofiler package. …”
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Differential expressed genes (DEGs) and differential alternative splicing genes (DASs) revealed the common pathologic mechanism of three bacterial pathogens to American eels (Angui... by Zihao Chen, Guanghua Sun, Songlin Guo

“…Compared to the Con group, result of the RNA-seq of six infected groups showed 2247 common differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis identified 23 common terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted 18 common pathways. …”
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SUGT1 is a prognostic biomarker and is associated with immune infiltrates in ovarian cancer by Linyan Ge, Xiu Liu, Lingyan Zhang, Jiaren Zhang, Guanghui Song

“…Methods We conducted a comprehensive bioinformatics analysis of SUGT1 expression in patients with OC compared with their normal controls, including the data from the cancer genome atlas (TCGA), genotype–tissue expression (GTEx) databases, gene ontology (GO) analysis, Kyoto Encylopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analysis (GSEA), single sample gene set enrichment analysis (ssGSEA). …”
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Proteome differences of dental stem cells between permanent and deciduous teeth by data-independent acquisition proteomics by Zhang Suping, Liu Yuqing, Dong Jin, Jiao Min, Gu Yongchun, Chen Liling, Yuan Na, Wang Jianrong, Yang Dezhao, Meng Fanwen

“…By comparing their expression levels, 209 differentially expressed proteins were identified. Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, along with protein–protein interaction network construction, revealed significant metabolic differences and key regulatory nodes. …”
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Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins by Kazuma Yoshioka, Reiko Nakagawa, Chi Lieu Kim Nguyen, Hayate Suzuki, Kiyohiro Ishigaki, Seiya Mizuno, Tsukasa Okiyoneda, Shizufumi Ebihara, Kazuya Murata

“…Although there were no obvious differences in the interactome of USP46 between wildtype and ΔK92, a gene ontology analysis revealed that centrosome‐related proteins were significantly enriched in the proximal proteins of USP46. …”
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Clinical Value and Potential Mechanism of miRNA-33a-5p in Lung Squamous Cell Carcinoma by Xiang-Ming Wang, Shang-Wei Chen, Gang Chen, Hua-Fu Zhou, Ting-Qing Gan, Jing-Jing Zeng, Zu-Yun Li

“…The differentially expressed genes (DEGs) of LUSC and the candidate target genes of miRNA-33a-5p were overlapped to acquire a set of specific genes for further analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and protein–protein interaction (PPI) network. miRNA-33a-5p overexpressed in LUSC was supported by 706 LUSC and 261 non-LUSC samples gathering from RT-qPCR, miRNA-seq, and public miRNA microarrays. …”
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胚胎干细胞分化为表皮样细胞的基因表达谱差异研究

“…结果：芯片筛选结果显示，分化后的ELC与ESC间的差异表达的基因多达4856个（Cut off：2）。基因本体（Gene Ontology，GO)分析显示与生物学过程（Biological Process,BP）相关的差异表达基因最多的是细胞过程（cellular process，CP），1931个；与亚细胞组分（Cellular Component, CC）相关的差基因中最多的是细胞和细胞组分（Cell, Cell part）相关基因，2391个；与分子功能（Molecular Function, MF）相关的差异基因中最多是的结合功能(binding)基因，1869个。…”
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Mediating Mendelian randomization in the proteome identified potential drug targets for obesity-related allergic asthma by Jiannan Lin, Shuwen Lu, Xiaoyu Zhao

“…We further explored the functions and enriched pathways of the mediating proteins using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. …”
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WNT3A promotes the cementogenic differentiation of dental pulp stem cells through the FOXO1 signaling pathway by Dongmei Cheng, Yang Bao, Xue Wang, Haidong Xiang, Tianyuan Guo, Yong Du, Zhiyong Zhang, Han Guo

“…Pathway enrichment exploration was conducted utilizing gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Metascape tools. …”
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Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease by Daisuke Yoshihara, Masanori Kugita, Tamio Yamaguchi, Harold M. Aukema, Hiroki Kurahashi, Miwa Morita, Yoshiyuki Hiki, James P. Calvet, Darren P. Wallace, Takafumi Toyohara, Takaaki Abe, Shizuko Nagao

“…By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 downregulated gene ontology biological process gene sets and six of the top 20 curated gene set canonical pathways identified to be downregulated by PIOtreatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. …”
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Network Pharmacology and Molecular Docking Study on the Mechanism of the Therapeutic Effect of Strychni Semen in NSCLC by He Geng, Yujie Xue, Binghua Yan, Zhaoxue Lu, Hengjin Yang, Peng Li, Jundong Zhou

“…The Protein-Protein Interaction (PPI) network was subsequently constructed to deeply analyse the interrelationship of the intersection targets via the String database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out via the Metascape database. …”
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Deciphering the multifaceted mechanism of Shuang Huang Lian in treating upper respiratory tract infections: A metabolomics-based network pharmacology approach by Gang Xu, Akshay Suresh Patil, Ruhan Wei, Dan Liu, Aimin Zhou, Yan Xu

“…A protein-protein interaction (PPI) network was constructed, and gene ontology (GO), KEGG, and Reactome enrichment analyses were conducted to elucidate the biological functions relevant to URTIs. …”
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Mechanistic insights into Y-Box binding protein-1 mediated regulation of lipid metabolism and oxidative stress in NAFLD via INHBE/TNF-β pathway by Zhi Ren, Rui Wang, Jun Wei, Zhenzeng Ma, Xiquan Ke

“…RNA sequencing was performed, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and protein-protein interaction (PPI) network analyses to identify differentially expressed genes (DEGs). …”
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Identification of candidate genes involved in Zika virus-induced reversible paralysis of mice by John D. Morrey, Venkatraman Siddharthan, Hong Wang, Alexandre L. R. Oliveira, Keiichiro Susuki, Rakesh Kaundal, Sara M. Freeman, Aaron J. Thomas, Naveen Duhan, Nathan G. Corry

“…To refine the search for candidate DEGs we used gene ontology analysis and RT-qPCR to select 3 DEGs that could be involved with the node of Ranvier function and 5 DEGs that could be involved with synaptic function. …”
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Genetic Mapping for Seed Aging Tolerance Under Multiple Environments in Sweet Corn by Yanchao Du, Jianting Lin, Haoxuan Jiang, Huating Zhao, Xuebiao Zhang, Ruigang Wang, Faqiang Feng

“…Candidate genes were explored within QTL cluster regions based on the aging-induced transcriptomic sequencing data of K62 and K107. Through Gene Ontology enrichment, gene annotation, and expression profiling clustering analyses, 12 positive candidate genes linked to seed aging tolerance were identified. …”
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