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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Constructing a metadata knowledge graph as an atlas for demystifying AI pipeline optimization by Revathy Venkataramanan, Revathy Venkataramanan, Aalap Tripathy, Tarun Kumar, Sergey Serebryakov, Annmary Justine, Arpit Shah, Suparna Bhattacharya, Martin Foltin, Paolo Faraboschi, Kaushik Roy, Amit Sheth

“…In this study, we present a solution by introducing Common Metadata Ontology (CMO) which is used to construct an extensive AI Pipeline Metadata Knowledge Graph (AIMKG) consisting of 1.6 million pipelines. …”
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纳米孔长读测序鉴定肝癌细胞中低氧特异性转录本 by 高力, 沈晟齐, 高平

“…结果本研究成功构建了基于纳米孔三代测序技术的低氧转录本数据集，展现了前所未有的测序精度。通过GO（gene ontology）富集分析，我们系统地挖掘了参与低氧响应的关键生物通路（<italic>P</italic>＜0.05）。…”
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Identification of Critical Signature in Post‐Traumatic Stress Disorder Using Bioinformatics Analysis and in Vitro Analyses by Lifen Liu, Yang Liu, Rui Li, Yue Teng, Shuyang Zhao, Jinhong Chen, Changjiang Li, Xinyu Hu, Lin Sun

“…Weighted gene co‐expression network analysis (WGCNA) was employed to examine gene correlation patterns. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for functional annotation and enrichment analysis, respectively. …”
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Exploring the inhibitory effect and mechanism of isorhamnetin therapy on oral squamous cell carcinoma based on network pharmacology and molecular docking by YU Fangfang, ZHOU Jingjing, YANG Jie, QU Huijuan, HUI Guangyan

“…At the same time, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) were used to analyze the related signaling pathways of the intersection targets. …”
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Potential Value of Circular RNA circTBC1D4 in Gastrointestinal Stromal Tumors by null Chunyan-Zou, null Yanpeng-He, null Changshun-Xie, null Fulai-Gao, null Xiaoli-Xie, null Xiukun-Chai, null Chenxi-He, null Dongqiang-Zhao

“…Furthermore, a circRNA-miRNA-mRNA network was established. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were used to reveal the correlation between the functions of signaling pathways and target genes. …”
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Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer by Xiao K. Ran, Xiao F. Zhao, Zhen W. Wei, Hua Z. Pang, Yan F. Tang, Rong Liu, Tie X. Wu, Xu D. Liu

“…Full transcript sequencing was used to analyze the RNA in the samples. Geno Ontology enrichment and Kyoto Encyclopedia of Genes and Genome pathway analyses were performed on differentially expressed eccDNA-related genes. …”
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Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer’s disease by Waimao Gao, Guang Yang, Xinjuan Liu, Kaifan Hu, Jie Pan, Xingyu Wang, Yan Zhao, Ying Xu

“…Then we performed Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses on these common targets. …”
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Thyroid hormone receptor- and stage-dependent transcriptome changes affect the initial period of Xenopus tropicalis tail regeneration by Shouhong Wang, Liezhen Fu, Bin Wang, Yanmei Cai, Jianping Jiang, Yun-Bo Shi

“…Results We discovered that GO (gene ontology) terms related to inflammatory response, metabolic process, cell apoptosis, and epithelial cell migration were highly enriched among commonly regulated genes during wound healing at either stage 56 or 61 or with either wild type (WT) or TRDKO tadpoles, consistent with the morphological changes associated with wound healing occurring in both regenerative (WT stage 56, TRDKO stage 56, TRDKO stage 61) and nonregenerative (WT stage 61) animals. …”
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Identification of core biomarkers for tuberculosis progression through bioinformatics analysis and in vitro research by Zhanpeng Chen, Qiong Wang, Quan Ma, Jinyun Chen, Xingxing Kong, Yuqin Zeng, Lanlan Liu, Shuihua Lu, Xiaomin Wang

“…We define genes with a P-value less than 0.05 for the combined effect of infection and time on gene expression as those with altered expression patterns. Gene Ontology (GO) enrichment analysis revealed that the biological functions of these genes mainly involve DNA translation, RNA processing, and transcriptional regulation. …”
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Reflections on the Yoruba Past: Toyin Falola on Isaac Delano by Wale Oyedeji

“…Leaning on the works of Isaac Delano, this work will look into the Yoruba past to reflect on the culture, philosophy, ideology, epistemology and ontology of the people, with a view to educating the general public on the inexhaustible items of their knowledge economy and productions. …”
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LIPUS promotes osteogenic differentiation of rat BMSCs and osseointegration of dental implants by regulating ITGA11 and focal adhesion pathway by Chao Liang, Yuqing Zhang, Yuwei Yan, Wei Geng, Jun Li, Xiu Liu

“…Micro-CT and toluidine blue staining were used to assess implant osseointegration. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to identify enriched functional terms and signalling pathways for differentially expressed genes from LIPUS-treated rat BMSC RNAseq data obtained from the GEO database. …”
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Identification of the Transcriptional Networks and the Involvement in Angiotensin II-Induced Injury after CRISPR/Cas9-Mediated Knockdown of Cyr61 in HEK293T Cells by Junjie Wang, Dongdong Fu, Soulixay Senouthai, Yan Jiang, Rentong Hu, Yanwu You

“…HEK293T cells were cultured, and Cyr61 knockdown was achieved by transfection of the CRISPR/Cas9 KO plasmid. lncRNA and mRNA microarrays were used to identify differentially expressed genes (DEGs). Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to determine biofunctions and signaling pathways. …”
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Adjunctive diagnostic tool for histopathological classification of congenital mesoblastic nephroma based in molecular genetic findings by Hiroshi Hamada, Kenichi Kohashi, Takeshi Iwasaki, Mikiko Hashisako, Yuko Hino, Masahiro Fukuhara, Amane Kamouchi, Naonori Kawakubo, Tatsuro Tajiri, Yoshinao Oda

“…Results PCA revealed differences in mutation patterns between the EGFR-ITDs and NTRK fusion tumor groups. Gene ontology analysis of the highly expressed genes in the EGFR-ITDs tumor group revealed enrichment related to the mitogen-activated protein kinase (MAPK) signaling pathway. p-Mek1/2 and p-Erk1/2 immunoreactivity was significantly increased in the EGFR-ITDs tumor group (p = 0.018 and p = 0.017, respectively). …”
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Grammar-constrained decoding for structured information extraction with fine-tuned generative models applied to clinical trial abstracts by David M. Schmidt, Philipp Cimiano

“…Toward this goal, we consider the task of inducing structured representations from abstracts describing clinical trials, relying on the C-TrO ontology to semantically describe the clinical trials and their results. …”
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Decreased Spp1 Expression in Acute Myocardial Infarction after Ischemia and Reperfusion Injury by Ling Li, Jungang Huang, Zongkai Zhao, Zhuzhi Wen, Kang Li, Tianjiao Ma, Lisui Zhang, Junmeng Zheng, Shi Liang

“…We used the GSE83472 dataset from the Gene Expression Omnibus (GEO) database to find differential RNA expression between ischemia-reperfusion tissue and control samples. In addition, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to find the biological property of 449 RNAs from GSE83472 via the Database for Annotation, Visualization, and Integrated Discovery (DAVID). …”
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Analysis of gene expression difference and biological process in chorionic villi of unexplained recurrent spontaneous abortion by Linling Shi, Lun Wei, Meiqiu Lu, Hongmei Ding, Le Bo

“…Differentially expressed genes were analyzed by the “Limma” package in R Studio, and Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were carried out with “Cluster Profiler” and “org.hs.eg.db” packages. …”
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Age-related changes in DNA methylation in a sample of elderly Brazilians by Hayley Welsh, Caio M. P. F. Batalha, Weili Li, Nadja C. Souza-Pinto, Yeda A. O. Duarte, Michel S. Naslavsky, Esteban J. Parra

“…Differentially methylated regions (DMRs) were also identified using DMRcate. Gene ontology (GO) pathway enrichment analyses were performed to explore the functional significance of identified DMPs and DMRs. …”
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Aberrant Expression of JAM2 Inhibits Invasion and Migration in Lung Adenocarcinoma by Jun Chen, Yuan Cui, Zhimeng Chen, Hao Ding, Chang Li, Sheng Ju, Cheng Ding, Chun Xu, Jun Zhao, Xin Tong

“…Materials Immunohistochemistry (IHC) was performed on 37 pairs of LUAD tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted among co‐expression genes in different JAM2 subgroups. …”
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iTRAQ-based quantitative proteomic analysis of herbicide stress in Avena ludoviciana Durieu by Hossein Adim, Leila Fahmideh, Barat Ali Fakheri, Hamid Najafi Zarrini, Hamidreza Sasanfar

“…Additionally, 138 differentially expressed proteins (DEPs) were identified in the resistant biotype (R), while 93 DEPs were identified in the susceptible biotype (S). Gene Ontology (GO) analysis revealed that these DEPs mainly consisted of proteins related to photosynthesis, respiration, amino acid synthesis and translation, secondary metabolite biosynthesis, defense proteins, and detoxification. …”
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