Identification of crucial extracellular genes as potential biomarkers in newly diagnosed Type 1 diabetes via integrated bioinformatics analysis by Ming Gao, Qing Liu, Lingyu Zhang, Fatema Tabak, Yifei Hua, Wei Shao, Yangyang Li, Li Qian, Yu Liu

“…Using R software, we screened out the extracellular protein-differentially expressed genes (EP-DEGs) through several protein-related databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to describe the role and function of these EP-DEGs. …”
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Candidate Genes Associated with Delayed Neuropsychomotor Development and Seizures in a Patient with Ring Chromosome 20 by Thiago Corrêa, Amanda Cristina Venâncio, Marcial Francis Galera, Mariluce Riegel

“…The candidate genes may play an important role in the developmental delay and seizures observed in r20 patients. Gene ontology included microtubule-based movement, nucleosome assembly, DNA repair, and cholinergic synaptic transmission. …”
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Comparative transcriptome analysis of albino northern snakehead (Channa argus) reveals its various collagen-related DEGs in caudal fin cells. by Shixi Chen, Ning Li, Fardous Mohammad Safiul Azam, Li Ao, Na Li, Jianlan Wang, Yuanchao Zou, Rui Li, Zakaria Hossain Prodhan

“…A total of 137,130 unigenes were identified in this study. Gene Ontology (GO) analysis showed that the identified DEGs were significantly enriched in cellular components related to cytoplasm. …”
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Proteomic Analysis of the Murine Liver Response to Oral Exposure to Aflatoxin B1 and Ochratoxin A: The Protective Role to Bioactive Compounds by Silvia Trombetti, Alessandra Cimbalo, Michela Grosso, Pilar Vila-Donat, Jordi Mañes, Lara Manyes

“…For proteomics analysis, peptides were separated using a LC-MS/MS-QTOF system and differentially expressed proteins (DEPs) were statistically filtered (<i>p</i> < 0.05) distinguishing males from females. Gene ontology visualization allowed the identification of proteins involved in important biological processes such as the response to xenobiotic stimuli and liver development. …”
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A Study of the Roots of Folding Urbanism Based on the Genealogy of Michel Foucault by arsalan Karimi khiavi, Siamak Panahi, Shahab Kariminia

“…In the field of urban planning of these relations, the ontology of urban topology layers according to Riemannian equations and Deleuze philosophy in the works of architects such as Peter Eisenman, Zaha Hadid, Eric Owen Moss, Charles Jenks, James Wines.  …”
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Molecular Networks Involved in the Immune Control of BK Polyomavirus by Eva Girmanova, Irena Brabcova, Jiri Klema, Petra Hribova, Mariana Wohlfartova, Jelena Skibova, Ondrej Viklicky

“…., CD40/CD40L; P<0.05). Gene ontology analysis revealed several biological networks associated with BKV immune control in comparison to the control group. …”
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Quantitative Evaluation of Vocabulary Emotional Color in Language Teaching by Zhong Caihong

“…Based on the research of modern Chinese ontology and the existing research results in the field of teaching Chinese as a foreign language, this paper takes the theory of interlanguage and transfer theory as the theoretical basis and mainly uses the methods of comparative analysis and error analysis to try to find out the relationship between emotional color teaching and acquisition. …”
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Network pharmacology combined with experimental verification for exploring the potential mechanism of phellodendrine against depression by Lili Hu, Na Wu, Jue Wang, Donghui Cai

“…The intersection targets between PHE and MDD were obtained to identify as targets for PHE against MDD, followed by protein–protein interaction network, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. …”
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Circular RNA microarray expression profile and potential function of circDOCK1 in colorectal cancer by Guojing Zhang, Xiaoyan Wu, Hongmin Fu, Daqing Sun

“…This study aimed to investigate the impact of circDOCK1 on CRC metastasis and prognosis as well as its underlying molecular mechanisms.MethodsWe explored circRNA expression profiles in four pairs of CRC tissues and adjacent non-carcinoma tissues via microarray analysis. After Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and circRNA–miRNA network analyses, circDOCK1 was chosen for further investigation. …”
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Bioinformatics approach reveals the critical role of inflammation-related genes in age-related hearing loss by Xi Gu, Chenyu Chen, Yuqing Chen, Chaojun Zeng, Yanchun Lin, Ruosi Guo, Shujin Xu, Chang Lin

“…The IRDEGs were mainly enriched in MAPK, PI3K-Akt, Hippo and JAK-STAT pathways by analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. …”
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Repurposing antiviral drugs targeting the PARP-1 and HER2 pathways with multifaceted impacts through integrated network analysis and molecular mechanics by Uma Maheshwari Mugundan, Praveen Sekar, Rajanandh Muhasaparur Ganesan

“…Through the application of network pharmacology, gene ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, this study identified Human Epidermal Growth Factor Receptor 2 (HER2) and Poly [ADP ribose] polymerase 1(PARP-1) as key targets involved in the molecular pathways associated with breast cancer. …”
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Effect of Mitochondrial Tu Translation Elongation Factor on Water-holding Capacity of Qinchuan Cattle Meat during Postmortem Aging by SI Jianfang, ZHANG Jing, GAO Shuang, MA Jiarong, CAO Songmin, LI Yalei, LUO Ruiming

“…Through proteomics, 23 differential proteins related to TUFM were identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the differential proteins could mediate cellular autophagy by participating in energy metabolism through a variety of pathways. …”
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Pilot study: Initial investigation suggests differences in EMT-associated gene expression in breast tumor regions by Kylie L. King, Hamed Abdollahi, Zoe Dinkel, Alannah Akins, Homayoun Valafar, Heather Dunn

“…All significant genes were analyzed for pathway enrichment using MSigDB and Gene Ontology databases, most notably the epithelial to mesenchymal transition and cell motility pathways. …”
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Blood transcriptome resources of chinstrap () and gentoo () penguins from the South Shetland Islands, Antarctica by Bo-Mi Kim, Jihye Jeong, Euna Jo, Do-Hwan Ahn, Jeong-Hoon Kim, Jae-Sung Rhee, Hyun Park

“…Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. …”
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Fracture-healing effects of Rhizoma Musae ethanolic extract: An integrated study using UHPLC-Q-Exactive-MS/MS, network pharmacology, and molecular docking. by Jian Zhang, Wanyan Shen, Fanzhi Liu, Hehe He, Shuquan Han, Lina Luo

“…Topological analysis of the protein-protein interaction (PPI) network identified 59 core targets, including key proteins like AKT1, IL-6, and EGFR, known for their anti-inflammatory properties and ability to enhance bone cell proliferation and differentiation. Gene Ontology analysis indicated the involvement of EERM in biological processes such as peptidyl-serine phosphorylation, response to xenobiotic stimulus, and nutrient level regulation. …”
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Proteomic characterization of molecular mechanisms of paraquat-induced lung injury in a mouse model by Yu Qing Zhou, Jin Jin Peng, Li Ping Shan, Wei Liu

“…Results The expression of 91, 160, and 78 proteins was significantly altered at days 2, 7, and 14, respectively. Gene Ontology analyses revealed that the DEPs in the PQ-2d and PQ-7d groups were involved primarily in humoral immunity and coagulation-related reactions, whereas those in the PQ-14d group were implicated primarily in chemotactic and regulatory responses. …”
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Validation and the role of PDK4 relevant to ferroptosis in degenerative lumbar disc disease by Wenhao Chen, Wanliang Yang, Bin Meng, Xingkun Wang, Heng Duan, Qian Xu, Hao Li

“…Method The differentially expressed genes (DEGs) in rat lumbar disc tissue between the control and IVDD group treated with IL-1β were detected by RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on DEGs. …”
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A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy by Qing Tang, Ying Xu, Canhui Deng, Chaohua Cheng, Zhigang Dai, Zemao Yang, Chan Liu, Jianguang Su

“…Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to “cell differentiation” and “cell cycle process,” as significant factors regulating apomeiosis. …”
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IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis by Qi Wang, Xufeng Huang, Shujing Zhou, Yuntao Ding, Huizhi Wang, Weiye Jiang, Min Xu

“…Based on the enrichment results of the “Gene Ontology“(GO) and “Kyoto Encyclopedia of Genes and genomes “(KEGG) as well as documented findings of key genes, we further emphasized the potential of IL1RN and PRRX1 as markers of immune infiltrates in CRC and confirmed our hypothesis by compiling data from the UALCAN, Tumor Immune Estimation Resource, and TISIDB databases for these two genes. …”
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Construction of an lncRNA-mediated ceRNA network to investigate the inflammatory regulatory mechanisms of ischemic stroke. by Meimei Xu, Shan Yuan, Xing Luo, Mengsi Xu, Guangze Hu, Zhe He, Xinyuan Yang, Rui Gao

“…This led to the establishment of a comprehensive lncRNA-miRNA-mRNA regulatory network comprising 12 lncRNAs, 16 sponge miRNAs, and 191 target mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that differentially expressed mRNAs (DEmRNAs) were significantly enriched in stroke-related pathways. …”
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