Transcriptome Analysis Reveals Complex Defensive Mechanisms in Salt-Tolerant and Salt-Sensitive Shrub Willow Genotypes under Salinity Stress by Dezong Sui, Baosong Wang

“…A comparative analysis between genotypes and time points showed 1,706 differentially expressed genes (DEGs), of which 1,029 and 431 DEGs were only found in the JW9-6 and JW2372, respectively. Gene Ontology (GO) and MapMan annotations suggested that many DEGs were involved in various defense-related biological pathways, including cell wall integrity, hormone signaling, antioxidant system, heat shock proteins, and transcription factors. …”
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Potential Biomarkers and Signaling Pathways Associated with the Pathogenesis of Primary Ameloblastoma: A Systems Biology Approach by Zeynab Bayat, Azin Mirzaeian, Amir Taherkhani

“…The Cytoscape software identified significant modules and the hub genes within the PPI network. Gene Ontology annotation and signaling pathway analyses were executed by employing the DAVID and Reactome databases, respectively. …”
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COMMUNICATION LEVELS OF THE INDIVIDUAL by V. M. Rubskyi

“…The philosophy of dialogue with the Other raises an equally important question about the conditions for the possibility of a metaphysical continuum in ontology, and in turn, suggests the acceptance of a philosophical premise about God as the space of subjectivity in the "I-You" dialogue. …”
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Comprehensive analysis of cuproptosis-related genes in immune infiltration and development of a novel diagnostic model for acute kidney injury by Yajing Li, Yingxue Ding

“…Our study aimed to investigate the involvement of cuproptosis-related genes (CRGs) in AKI.Methods Identification of CRGs was conducted using differential expression analysis, and subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using human sequencing profiles. …”
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Identification of Functional Modules and Key Pathways Associated with Innervation in Graft Bone—CGRP Regulates the Differentiation of Bone Marrow Mesenchymal Stem Cells via p38 MAP... by Ziqian Wu, Xudong Wang, Jingcun Shi, Anand Gupta, Yuhan Zhang, Bingqing Zhang, Yang Cao, Lei Wang

“…We identified differentially expressed genes) from these samples and used the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases for functional enrichment and signaling pathway analysis. …”
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Identification of Signal Pathways and Hub Genes of Pulmonary Arterial Hypertension by Bioinformatic Analysis by Rui-Qi Wei, Wen-Mei Zhang, Zhe Liang, Chunmei Piao, Guangfa Zhu

“…All the raw data were processed by R, and differentially expressed genes (DEGs) were screened out by the “limma” package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed and visualized by R and Cytoscape software. …”
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A Comparison of Computational Approaches for Intron Retention Detection by Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li

“…We also describe the use of differential analysis methods to identify disease-associated IRs and compare differential IRs along with their Gene Ontology enrichment, which is illustrated on an Alzheimer’s disease RNA-Seq dataset. …”
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Bioinformatics Analysis of Exercise-Related Biomarkers in Diabetes by Xiaoju Bao, Jingyue Qiu, Qin Xuan, Xinming Ye

“…Then, the enrichment analysis of DEGs in Gene Ontology (GO) function was analyzed by Metascape, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of DEGs was also analyzed by gene set enrichment analysis (GSEA). …”
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Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs by Young-Sup Lee, Donghyun Shin

“…We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. …”
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Perspectives on Clinical Informatics: Integrating Large-Scale Clinical, Genomic, and Health Information for Clinical Care by In Young Choi, Tae-Min Kim, Myung Shin Kim, Seong K. Mun, Yeun-Jun Chung

“…The representative standardization effort by the Clinical Bioinformatics Ontology (CBO) aims to provide uniquely identified concepts to include molecular pathology terminologies. …”
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Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes by Dhananjay Kumar, Dharmendra Singh, Pulkit Kanodia, Kumble Vinod Prabhu, Manish Kumar, Kunal Mukhopadhyay

“…We identified 1306 potential target genes for these 52 miRNAs with vital roles in response to stimuli, signaling, and diverse metabolic and cellular processes. Gene ontology analysis showed 66, 20, and 35 target genes to be categorized into biological process, molecular function, and cellular component, respectively. …”
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Identification of Differentially Expressed lncRNAs in a CpG ODN-Activated Macrophage by Ying Zheng, Xi Luo, Zailong Qin, Zhiguang Zhou

“…The results revealed that expression levels of 734 lncRNAs and 734 mRNAs were altered at all time points. 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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RNA Sequencing Reveals the Differentially Expressed circRNAs between Stable and Unstable Carotid Atherosclerotic Plaques by Xueguang Lin, Ying Deng, Lujuan Ye, Bo Chen, Jindong Tong, Weijun Shi, Bo Wang, Bo Yu, Jingdong Tang

“…Functional evaluation of the DE circRNAs was conducted via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. …”
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A Method for Trust Quantification in Cloud Computing Environments by Xiaohui Li, Jingsha He, Bin Zhao, Jing Fang, Yixuan Zhang, Hongxing Liang

“…In this paper, we propose a method for trust quantification based on fuzzy comprehensive evaluation theory for cloud computing to protect user data through trust quantification of cloud services after we introduce trust ontology for cloud services and define user preference trust values. …”
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De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome by Vladimir A. Zhukov, Alexander I. Zhernakov, Olga A. Kulaeva, Nikita I. Ershov, Alexey Y. Borisov, Igor A. Tikhonovich

“…As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. …”
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Deciphering the dose-dependent effects of thymoquinone on cellular proliferation and transcriptomic changes in A172 glioblastoma cells. by Rachana Pandey, Purushothaman Natarajan, Umesh K Reddy, Wei Du, Cristian Sirbu, Moussa Sissoko, Gerald R Hankins

“…We confirmed their expression levels through quantitative RT-PCR and performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for these DEGs. …”
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Prediction of influenza A virus-human protein-protein interactions using XGBoost with continuous and discontinuous amino acids information by Binghua Li, Xin Li, Xiaoyu Li, Li Wang, Jun Lu, Jia Wang

“…Finally, we successfully identified 3,269 potential target proteins. Gene ontology (GO) and pathway analysis showed that these genes were highly associated with IAV infection. …”
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Detection of HIV-1 and Human Proteins in Urinary Extracellular Vesicles from HIV+ Patients by Samuel I. Anyanwu, Akins Doherty, Michael D. Powell, Chamberlain Obialo, Ming B. Huang, Alexander Quarshie, Claudette Mitchell, Khalid Bashir, Gale W. Newman

“…Western blots confirmed the presence of HIV proteins. Gene ontology (GO) analysis was performed using FunRich and HIV Human Interaction database (HHID). …”
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Genetic analysis of ocular tumour-associated genes using large genomic datasets: insights into selection constraints and variant representation in the population by Jose S Pulido, Mandeep S Sagoo, Omar A Mahroo, Alexander Tanner

“…UniProt was used for further gene characterisation, and gene ontology Protein Analysis THrough Evolutionary Relationships was explored for common biological pathways. …”
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Identification of Differentially Expressed Genes in Pituitary Adenomas by Integrating Analysis of Microarray Data by Peng Zhao, Wei Hu, Hongyun Wang, Shengyuan Yu, Chuzhong Li, Jiwei Bai, Songbai Gui, Yazhuo Zhang

“…Gene function analysis including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) networks analysis was conducted to interpret the biological role of those DEGs. …”
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