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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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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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

“…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. Kyoto Encyclopedia of Genes and Genomes analyses indicated that complement and coagulation cascades were key pathways in the PQ-2d and PQ-7d groups, whereas xenobiotic metabolism by cytochrome P450 was a key pathway in the PQ-14d group. …”
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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

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on DEGs. …”
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Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis by Jie Zhao, Ying-Hui Zhou, Ya-Qiong Zhao, Yao Feng, Fei Yan, Zheng-Rong Gao, Qin Ye, Yun Chen, Qiong Liu, Li Tan, Shao-Hui Zhang, Jing Hu, Marie Aimee Dusenge, Yun-Zhi Feng, Yue Guo

“…The linear discriminant analysis effect size showed that the most representative biomarkers were the genus Haemophilus in males, whereas the dominant bacteria in females were Campylobacter. Kyoto Encyclopedia of Genes and Genomes analysis showed that predicting changes in the female oral microbiota may be related to the immune system and immune system diseases are the main factor in males. …”
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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

“…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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High Expression of UPK3A Promotes the Progression of Gastric Cancer Cells by Inactivating p53 Pathway by Deliang Xu, Jing Guo, Hongwei Xu

“…Silencing of UPK3A inhibited the proliferation, migration, and invasion of gastric cancer cells. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that UPK3A was involved in the p53 signaling pathway. …”
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Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer by Qin Bian, Haijun Li, Xiaoyi Wang, Tingting Liang, Kai Zhang

“…Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis were used for functional enrichment analysis of DEGs. …”
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Identification of retinol dehydrogenase 10 as a shared biomarker for metabolic dysfunction-associated steatotic liver disease and type 2 diabetes mellitus by Fangyu Li, Rui Li, Hongjun Deng

“…We also analyzed the enriched pathways of shared genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Next, hub gene validation was performed using the least absolute shrinkage and selection operator (LASSO) and receiver operating characteristic (ROC) curves. …”
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Formation mechanisms of ethyl acetate and organic acids in Kluyveromyces marxianus L1-1 in Chinese acid rice soup by Na Liu, Likang Qin, Laili Hu, Song Miao

“…At least 4231 genes and 2937 proteins were identified and 610 differentially expressed proteins were annotated to 30 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways based on the analysis results of transcriptome and proteome. …”
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Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease by Yeonjeong Heo, Jeeyoung Kim, Seok-Ho Hong, Woo Jin Kim

“…Functional analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Results scRNA-seq was used to analyze the transcriptome of peripheral blood mononuclear cells from seven normal controls and eight patients with COPD. …”
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Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics. by Wenlong Kuang, Jianwu Huang, Yulu Yang, Yuhua Liao, Zihua Zhou, Qian Liu, Hailang Wu

“…Differentially expressed genes (DEGs) in the dataset were screened by ClusterGVis, Weighted Gene Co-Expression Network Analysis (WGCNA) and GEO2R, and functional enrichment was performed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Genomes (KEGG). Then mitochondria-associated DEGs (MitoDEGs) were obtained. …”
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Comparative transcriptomic analysis of primary endometrial cancer and bone metastatic cancer: metastasis-associated genes and abnormal cell cycle regulation by Qinmin Wu, Feng Li, Yunlong Zhang, Siying Li, Chuan Xiang

“…E2F1, MCM2, RFC2, and ICAM1 are involved in the metastasis and progression of EC with bone metastasis (ECBM). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicates significant changes in the Hippo signaling pathway, which regulates cell proliferation, and in the cell adhesion signaling pathway. …”
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Interleukin-6 related signaling pathways as the intersection between chronic diseases and sepsis by Jie Yang, Lin Yang, Yanjiao Wang, Lu Huai, Bohan Shi, Di Zhang, Wei Xu, Di Cui

“…IL-6 related signaling pathways were sought in Kyoto Encyclopedia of Genes and Genomes (KEGG), and retrieved protein-protein interaction in the Search for Interaction Genes tool (STRING). …”
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Determining the Potential Roles of Branched-Chain Amino Acids in the Regulation of Muscle Growth in Common Carp (Cyprinus carpio) Based on Transcriptome and MicroRNA Sequencing by Xianglin Cao, Han Cui, Xinyu Ji, Baohua Li, Ronghua Lu, Yuru Zhang, Jianjun Chen

“…Based on their expression profiles, 2,146 differentially expressed genes (DEGs) and 84 differentially expressed miRNA (DEMs) were evaluated. Kyoto Encyclopedia of Genes and Genome pathways, including the proteasome, phagosome, autophagy in animals, proteasome activator complex, and ubiquitin-dependent protein catabolic process, were enriched for these DEGs and DEMs. …”
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Transcriptomics reveals substance biosynthesis and transport on membranes of Listeria monocytogenes affected by antimicrobial lipopeptide brevilaterin B by Yangliu Liu, Yawei Ning, Zhou Chen, Panpan Han, Tongxin Zhi, Siting Li, Aijin Ma, Yingmin Jia

“…Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that brevilaterin B influenced multiple pathways of L. monocytogenes, including peptidoglycan biosynthesis, membrane transport (ATP-binding cassette transports, ion transport), cellular metabolism (amino acid and lipid metabolism), ATP synthesis, and activation of the stress response (quorum sensing and bacterial chemotaxis). …”
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Elevated LIF and JAK-STAT activation drive severe COVID-19 in myeloma patients receiving the BCMA-CD3 bispecific antibody Elranatamab by Ziping Li, Fujing Zhang, Xianghong Jin, Junling Zhuang

“…Gene Ontology (GO) analysis revealed that DEPs between the BiTe and PI groups were related to cytokine activity and leukocyte migration. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEPs were enriched in cytokine-cytokine receptor interaction and JAK-STAT signaling pathways. …”
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An Integrated Approach Exploring the Synergistic Mechanism of Herbal Pairs in a Botanical Dietary Supplement: A Case Study of a Liver Protection Health Food by Liang Chen, Chun Hu, Molly Hood, Juntao Kan, Xiaona Gan, Xue Zhang, Yi Zhang, Jun Du

“…Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed along with network analysis. …”
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