Development of machine learning models for diagnostic biomarker identification and immune cell infiltration analysis in PCOS by Wenxiu Chen, Jianliang Miao, Jingfei Chen, Jianlin Chen

“…These differentially expressed genes (DEGs) were further analyzed for Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. …”
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Dual disease co-expression analysis reveals potential roles of estrogen-related genes in postmenopausal osteoporosis and Parkinson’s disease by Dongdong Yu, Dongdong Yu, Jian Kang, Chengguo Ju, Qingyan Wang, Ye Qiao, Ye Qiao, Long Qiao, Long Qiao, Dongxiang Yang

“…Differentially expressed genes (DEGs) among PMO, PD, and ERGs were subjected to an array of bioinformatics analyses, including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses, in addition to protein-protein interaction (PPI) network analysis. …”
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Involvement of Cholesterol Metabolic Pathways in Recovery from Noise-Induced Hearing Loss by Na Sai, Xi Shi, Yan Zhang, Qing-qing Jiang, Fei Ji, Shuo-long Yuan, Wei Sun, Wei-Wei Guo, Shi-Ming Yang, Wei-Ju Han

“…In total, 2,158 proteins were identified using iTRAQ. Both gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses showed that immune and metabolic pathways were prominently involved during the impairment stage of acute hearing loss. …”
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Identification and validation of the important role of KIF11 in the development and progression of endometrial cancer by Biying Wang, Lunmin Bao, Xiaoduo Li, Guang Sun, Wu Yang, Nanzi Xie, Ling Lei, Wei Chen, Hailong Zhang, Man Chen, Xing Zhao, Xiufang Wan, Rui Yuan, Hongmei Jiang

“…Functional enrichment analysis of the DEGs was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. …”
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Genome-wide association study of the antibody response to <i>Corynebacterium pseudotuberculosis</i> in sheep by J. Kyselová, L. Tichý, J. Marková, A. Gurgul, Z. Sztankóová, K. Vališ, S. Šlosárková, K. Kavanová, M. Beinhauerová, T. Szmatola, T. Szmatola

“…By analysing genomic alterations and their context between positive and negative animals, including a gene ontology (GO) analysis of genes within <span class="inline-formula">±</span> 500 kb regions of the suggestive SNPs, we identified genes and immune-related processes and pathways potentially influencing CLA susceptibility. …”
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Dysfunctional β-cell autophagy induces β-cell stress and enhances islet immunogenicity by Matthew C. Austin, Charanya Muralidharan, Saptarshi Roy, Justin J. Crowder, Jon D. Piganelli, Amelia K. Linnemann, Amelia K. Linnemann

“…Lastly, we co-cultured ATG7Δβ-cell islet cells with diabetogenic BDC2.5 helper T cells and evaluated T cell activation.ResultsWe found that all ATG7Δβ-cell mice developed diabetes between 11-15 weeks of age. Gene ontology analysis revealed a significant upregulation of pathways involved in inflammatory processes, response to ER stress, and the ER-associated degradation pathway. …”
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Adipose tissue may not be a major player in the inflammatory pathogenesis of Autism Spectrum Disorder by Baojiang Wang, Yueyuan Qin, Yong Chen, Xiujie Zheng, Yanjuan Chen, Juan Zhao, Feng Zhang, Shan Duan

“…The up-regulated differentially expressed genes from the GSE18123 dataset were subjected to gene ontology (GO) enrichment analysis to explore ASD-associated pathways. …”
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Transcriptomic and behavioral studies reveal that glutamate receptors are involved in depressive-like behavior in adult olive flounder Paralichthys olivaceus by Liangfang Liu, Tangsong Feng, Mengmeng Shi, Huafeng Zou, Weiqun Lu

“…Meanwhile glial fibrillary acidic protein, the biomarkers of astroglial pathology, and glutamatergic synaptic genes were significantly up-regulated in AG flounder. In addition, Gene Ontology (GO) enrichment analysis revealed that DEGs enriched in peptide biosynthetic process, translation procession were down-regulated in the AG flounder. …”
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O-GlcNAcylation attenuates ischemia-reperfusion-induced pulmonary epithelial cell ferroptosis via the Nrf2/G6PDH pathway by Liuqing Yang, Hexiao Tang, Jin Wang, Dawei Xu, Rui Xuan, Songping Xie, Pengfei Xu, Xinyi Li

“…Results First, we identified O-GlcNAc transferase 1 (Ogt1) as a differentially expressed gene in lung epithelial cells of acute lung injury/acute respiratory distress syndrome (ALI/ARDS) patients, using single-cell sequencing, and Gene Ontology analysis (GO analysis) revealed the enrichment of the ferroptosis process. …”
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Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients by Shi-Xia Liao, Lan-Ying Zhang, Ling-Mei Shi, Huai-Yu Hu, Yan-Hui Gu, Ting-Hua Wang, Yao Ouyang, Peng-Peng Sun

“…Functional enrichment analyses, including Gene Ontology (GO), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA), were performed. …”
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Construction of the bromodomain-containing protein-associated prognostic model in triple-negative breast cancer by Wei Chen, Yushuai Yu, Chenxi Wang, Zirong Jiang, Xiewei Huang, Yidan Lin, Hongjing Han, Qing Wang, Hui Zhang

“…Differentially expressed BRDRGs (DE-BRDRGs) were determined by overlapping DEGs1, DEGs2 and DEGs3. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis were conducted to investigate active pathways and molecular interactions. …”
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Transcriptomic analysis of melatonin on the mechanism of embryonic gonadal development in female Jilin white geese by Jin Yu, Ichraf Mabrouk, Qiuyuan Liu, Yuxuan Zhou, Yupu Song, Jingyun Ma, Fengshuo Liu, Xiangman Hu, Zhiyi Yang, Yuxia Zeng, Jingtao Hu, Yongfeng Sun

“…These DEGs were enriched in Gene Ontology (GO) terms related to the microtubule cytoskeleton, cytoskeleton, cell adhesion, and biological adhesion and the KEGG enrichment analysis suggested that the DEGs were mainly enriched in “MAPK signaling pathway”, “Wnt signaling pathway”, “Calcium signaling pathway”, “Focal adhesion”, “Neuroactive ligand-receptor interaction”, “Melanogenesis”, “mTOR signaling pathway”, “ECM-receptor interaction”, and “TGF-beta signaling pathway” in the two comparison groups. …”
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Network pharmacology and experimental verification reveal the mechanism of Qingfei Tongluo mixture in treating pulmonary fibrosis by Ying Zhou, Wenlong Wang, Wanping Zhu, Tingting Cai, Nannan Wang, Xia Liu, Wenmin Wang, Kequn Chai

“…Quercetin, a key active ingredient, was associated with the TGF-β1 signaling pathway. Gene Ontology and KEGG enrichment analyses identified 42 core genes, with a notable implication of the TGF-beta signaling pathway in PF. …”
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N6-methyladenosine methylation regulators can serve as potential biomarkers for endometriosis related infertility by Yalun He, Jie Ding, Tonglin Bai, Yangshuo Li, Xiaolan Liang, Yiming Chen, Yi Lin, Wen Cheng, Chaoqin Yu

“…The study identified seven key m6A regulators with significant diagnostic value for EMS-related infertility and two distinct m6A molecular clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs between the clusters revealed that m6A clustering was strongly associated with immune pathways. …”
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MAP17 is a Novel NASH Progression Biomarker Associated with Macrophage Infiltration, Immunotherapy Response, and Oxidative Stress by Huang Z, Chen J, Liu S, Xiang X, Long Y, Tan P, Fu W

“…Additionally, we conducted gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) to elucidate the mechanisms by which MAP17 operates. …”
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Integrated bioinformatics analysis and experimental validation of exosome-related gene signature in steroid-induced osteonecrosis of the femoral head by Renqun Mao, Wen Bi, Mengyue Yang, Lei Qin, Wenqing Li

“…Gene Set Variation Analysis (GSVA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to investigate latent enriched pathways. …”
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CYFIP2: potential pancreatic cancer biomarker and immunotherapeutic target by Cong Xiao, Xiaojuan Zhang, Bobo Hou, Ping Wan, Zhenjun Cao, Xuefeng Rao

“…The R packages “survminer” and “survival” were used to statistically analyze the relationship between CYFIP2 expression and the survival and prognosis of tumor patients. the R package “ss GSEA” was used to assess the correlation between CYFIP2 expression and immune infiltration. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Variation Analysis (GSVA) were used to explore the multiple biological functions and regulatory pathways in which CYFIP2 co-expressed genes co-engage in pancreatic cancer. …”
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Deletion of sphingosine 1-phosphate receptor 1 in myeloid cells reduces hepatic inflammatory macrophages and attenuates MASH by Gopanandan Parthasarathy, Nanditha Venkatesan, Guneet Singh Sidhu, Myeong Jun Song, Chieh-Yu Liao, Fanta Barrow, Amy Mauer, Tejasav Sehrawat, Yasuhiko Nakao, P. Vineeth Daniel, Debanjali Dasgupta, Kevin Pavelko, Xavier S. Revelo, Harmeet Malhi

“…As determined by mass cytometry, a significant decrease in recruited macrophages was noted in the livers of high-fat, -fructose, and -cholesterol–fed S1pr1 MKO mice compared to wild-type. Gene ontology pathway analysis revealed significant suppression of the peroxisome proliferator–activated receptor gamma and mitogen-activated protein kinase pathways in S1pr1 MKO consistent with attenuated MASH in mice. …”
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Exploring biomarkers and molecular mechanisms of Type 2 diabetes mellitus promotes colorectal cancer progression based on transcriptomics by Simin Luo, Yuhong Zhu, Zhanli Guo, Chuan Zheng, Xi Fu, Fengming You, Xueke Li

“…The key biological processes were screened by gene ontology and gene set enrichment analysis. A diagnostic model for co-morbidities was constructed by logistic regression model with least absolute shrinkage and selection operator (Lasso) regularization method. …”
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Identification of EARS2 as a Potential Biomarker with Diagnostic, Prognostic, and Therapeutic Implications in Colorectal Cancer by Wang L, Deng X, Tang J, Gong Y, Bu S, Li Z, Liao B, Ding Y, Dai T, Liao Y, Li Y

“…To investigate the mechanisms underlying EARS2 in CRC, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis, and Protein-Protein Interaction analyses were performed, alongside the construction of miRNA-mRNA interaction networks. …”
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