Single-cell atlas reveals multi-faced responses of losartan on tubular mitochondria in diabetic kidney disease by Zhen Zhu, Guangxin Luan, Song Wu, Yiyi Song, Shuang Shen, Kaiyue Wu, Shengnan Qian, Weiping Jia, Jun Yin, Tao Ren, Jianping Ye, Li Wei

“…Results Through the single-cell atlas of DKD mouse kidneys, it was found that losartan treatment significantly increased the percentage of PT cells. Gene Ontology (GO) enrichment analysis of differentially expressed genes showed enrichment of autophagy of mitochondrion pathway. …”
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The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer by Yao Yi, Yao Yi, Yu Zhong, Yu Zhong, Lianhua Xie, Lianhua Xie, Shuxian Lu, Shuxian Lu, Yifeng Zhang, Yifeng Zhang

“…Therefore, there is an urgent need to discover novel and targeted therapeutic strategies, particularly those focusing on the immune infiltrate in TNBC, to enhance diagnosis and prognosis for affected individuals.MethodsThe gene co-expression network and gene ontology analyses were used to identify the differential modules and their functions based on the GEO dataset of GSE76275. …”
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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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Logical reasoning for human activity recognition based on multisource data from wearable device by Mahmood Alsaadi, Ismail Keshta, Janjhyam Venkata Naga Ramesh, Divya Nimma, Mohammad Shabaz, Nirupma pathak, Pavitar Parkash Singh, Sherzod Kiyosov, Mukesh Soni

“…In order to realize the natural fusion of signal processing and logical reasoning in behavior recognition research, this work designs a lightweight behavior recognition solution using the pertinent theories of ontology reasoning in classical artificial intelligence. …”
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Network Pharmacology Analysis of the Identification of Phytochemicals and Therapeutic Mechanisms of Paeoniae Radix Alba for the Treatment of Asthma by Jingwei Wang, Ling Peng, Lu Jin, Huiying Fu, Qiyang Shou

“…Target protein interaction (PPI) network was constructed through the STRING database. The Gene Ontology (GO) biological process and Kyoto Encyclopedia of Genes and Genes (KEGG) pathway enrichment analysis were analyzed through the biological information annotation database (DAVID). …”
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Anaplasma phagocytophilum AFAP targets the host nucleolus and inhibits induced apoptosis by Daxiu Zhang, Lifeng Yu, Hui Tang, Hua Niu, Hua Niu, Hua Niu

“…A total of 586 host proteins were identified interacting with AFAP by data-independent acquisition mass spectrometry and annotated to 501 Gene Ontology (GO) terms, with the significantly over-represented ones related to ribosomes, nucleolus, DNA binding, and rRNA metabolic process. …”
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RBM47 is a novel immunotherapeutic target and prognostic biomarker in gliomas by Wei Wei, Yongfu Cao, Xin Lu, Long Wang, Jianbin Li, Guojun Deng, Donghai Li, Limin Xiao

“…The nomogram combining RBM47 expression levels with clinical prognostic factors demonstrated strong predictive accuracy, achieving a C-index of up to 0.863 in both TCGA training and CGGA validation groups. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Variation Analysis indicated that RBM47 is closely related to immunity and inflammation. …”
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Entre sacrificios y esperanzas: análisis de conflictos socioambientales en Bogotá desde una perspectiva de ecología política by Mariluz Nova Laverde, Milton Piñeros Fuentes, Jaime Edison Rojas Mora

“…This research contributes to critical geography, rural studies, and environmental justice by incorporating relational ontologies and a decolonial and ecofeminist perspective.…”
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Whole-Genome Expression Analysis and Signal Pathway Screening of Synovium-Derived Mesenchymal Stromal Cells in Rheumatoid Arthritis by Jingyi Hou, Yi Ouyang, Haiquan Deng, Zhong Chen, Bin Song, Zhongyu Xie, Peng Wang, Jinteng Li, Weiping Li, Rui Yang

“…Our results showed that there were 4828 differentially expressed genes in the RA group compared to the HD group; 3117 genes were upregulated, and 1711 genes were downregulated. A Gene Ontology analysis showed significantly enriched terms of differentially expressed genes in the biological process, cellular component, and molecular function domains. …”
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Integrated Bioinformatics-Based Identification of Potential Diagnostic Biomarkers Associated with Diabetic Foot Ulcer Development by Long Qian, Zhipeng Xia, Ming Zhang, Qiong Han, Die Hu, Sha Qi, Danmou Xing, Yan Chen, Xin Zhao

“…These DEGs were then arranged into a protein-protein interaction (PPI) network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analyses were performed to explore the functional roles of these genes. …”
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High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute by Md. Tariqul Islam, Ahlan Sabah Ferdous, Rifat Ara Najnin, Suprovath Kumar Sarker, Haseena Khan

“…For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. …”
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Identifying ADME-related gene signature for immune landscape and prognosis in KIRC by single-cell and spatial transcriptome analysis by Hongyun Wang, Feizhou Li, Qiong Wang, Xinyuan Guo, Xinbing Chen, Xinrong Zou, Jun Yuan

“…Multivariate analysis confirmed the independent predictive ability of ARPS, and an ARPS-based nomogram was constructed for clinical application. Gene ontology and KEGG pathway analyses revealed immune-related functions and pathways enriched in these groups, with low-risk patients showing better responses to immunotherapy. …”
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Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS by Ji-sun Kwon, Jihye Kim, Dougu Nam, Sangsoo Kim

“…GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. …”
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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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Identification of Aberrantly Expressed miRNAs in Gastric Cancer by Dan Liu, Xiaowei Hu, Hongfeng Zhou, Guangyue Shi, Jin Wu

“…We found that 31 miRNAs are upregulated in gastric cancer (P<0.05) and 10 miRNAs have never been reported by other studies; 30 miRNA are downregulated (P<0.05) in gastric cancer tissues. Gene ontology analysis revealed that those dysregulated miRNAs mainly take part in regulating cell proliferation. …”
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A practical approach to building a calcareous nannofossil knowledge graph by Hongyi Zhao, Bin Hu, Chao Ma, Shijun Jiang, Yi Zhang, Xin Li, Lirong Chen, Can Cai, Longgang Ye, Shengjian Zhou, Chengshan Wang

“…By delving into the structured data associated with calcareous nannofossil biozones (the UC zone, CC zone and NC zone), we propose an ontology to describe the semantic units and logical relationships of paleontological biozones and species and then integrate relevant species records from unstructured research reports to construct a knowledge graph for calcareous nannofossils, that integrates multisource paleobiological data and knowledge reconstruction. …”
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Genome-Wide Identification of the ABC Gene Family in Rosaceae and Its Evolution and Expression in Response to Valsa Canker by Chenglong Du, Hongqiang Yu, Huanhuan Hu, Zhiqi Dou, Cunwu Zuo, Junqiang Niu

“…In pears, gene pairs produced by WGD underwent purifying selection. Gene ontology (GO) enrichment analysis indicated the involvement of ABC proteins in transmembrane transport and signal transduction pathways. …”
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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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Transcriptomic analysis reveals the crucial role of YABBY genes family in hormonal induced parthenocarpy in Cucumis sativus L. by Tingting Liu, Rahat Sharif, Zetao Shi, Kehong Guo, Zhisen Zhang, Xueping Bao, Ahmad Ali

“…The cis-elements and gene ontology (GO) analysis revealed the involvement of CsYABBY genes in vegetative growth and the transition of vegetative to the reproductive phase. …”
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Consistent RNA expression and RNA modification patterns in cardiotoxicity induced by Matrine and Evodiamine by Guanhua Fang, Guanhua Fang, Yanming Shen, Xinyue Gao, Lele Yang, An Zhu, Dongshan Liao, Dongshan Liao

“…Based on our sequencing results, we observed consistent patterns of gene expression and epitranscriptome regulation (m6A and A-to-I modifications) across various drugs-treated AC16 cells when analyzed using KEGG pathway enrichment and gene ontology analyses. Furthermore, m6A writers VIRMA and A-to-I writers ADARB1 is consistent target of Evodiamine and Matrine. …”
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