Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle by Yan Peng, Xianwen Zhang, Yuewu Liu, Xinbo Chen

“…Finally, a heat-induced miRNA-PPI (protein-protein interaction) network was constructed, and three miRNA coregulatory modules were discovered.…”
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Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling by Chaofan Shan, Kui Dong, Dongyu Wen, Ziyi Ye, Fei Hu, Meryem Zekraoui, Jun Cao

“…Furthermore, the protein interaction network revealed their interactions with a number of proteins of significant functional importance. …”
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Identification of Key Genes and Prognostic Value Analysis in Hepatocellular Carcinoma by Integrated Bioinformatics Analysis by Meng Wang, Licheng Wang, Shusheng Wu, Dongsheng Zhou, Xianming Wang

“…The functional and pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of the identified DEGs was constructed using the Search Tool for the Retrieval of Interacting Gene, and hub genes were identified. …”
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Orientin Reduces the Effects of Repeated Procedural Neonatal Pain in Adulthood: Network Pharmacology Analysis, Molecular Docking Analysis, and Experimental Validation by Dong-Dong Guo, Hai-Yan Huang, Hai-E. Liu, Kun Liu, Xing-Jing Luo

“…Several compound-protein databases and disease-protein databases were employed to identify proteins that were both predicted targets of orientin and involved in neonatal pain. A protein-protein interaction (PPI) network was constructed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential mechanism of action. …”
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Salvage pathway of vitamin B12 absorption in chickens with mutant tumor virus a receptor by Yun Ji Shin, Jin-Kyoo Kim, Seung Je Woo, Byung Chul Park, Jae Yong Han

“…This study investigates the relationship between the various genotypes of TVA alleles and uptake of vitamin B12 in chickens. A protein interaction model suggested that mutant TVAs (i.e., TVASNP, TVAR) may have reduced ability to take up vitamin B12 due to a disrupted LDL-A domain, a pivotal region involved in vitamin B12 uptake; however, we found no significant difference in absorption of vitamin B12 in TVAWT and TVASNP chickens, or levels of its metabolite in serum. …”
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Elucidating the causal associations and mechanisms between circulating immune cells and idiopathic pulmonary fibrosis: new insights from Mendelian randomization and transcriptomics by Han Yang, Xuanyu Wu, Xiang Xiao, Jiajing Chen, Xiaomin Yu, Wen Zhao, Fei Wang

“…Subsequently, SNP-nearest genes combined with the transcriptomics data of IPF were subjected to multiple bioinformatics analyses such as TIMER, WGCNA, functional enrichment analysis, protein-protein interaction analysis, and ROC to identify IPF biomarkers. …”
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Compound exposure of 2.8 GHz and 9.3 GHz microwave causes learning and memory impairment in rats by Liu Sun, Xiaoya Wang, Ke Ren, Chuanfu Yao, Haoyu Wang, Xinping Xu, Hui Wang, Ji Dong, Jing Zhang, Binwei Yao, Xiaohui Wei, Ruiyun Peng, Li Zhao

“…Gene ontology (GO) and Protein-protein interaction (PPI) analyses of differential expressed genes (DEGs) in peripheral blood suggested that Htt and Bdnf might be potential indicators to predict microwave. …”
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Network pharmacology and molecular analysis of mechanisms underlying the therapeutic effects of Rhubarb in treating atherosclerosis and abdominal aortic aneurysm by Huilin Xu, Jun Huang, Youjie Zeng, Xia Wang, Huilin Lian, Siyi Zhang, Ren Guo

“…Gene interactions were utilized to identify common targets of Rhubarb with AS/AAA, and interaction networks were constructed using Cytoscape 3.9.1. Protein-protein interaction (PPI) networks for the core targets were constructed using the STRING database. …”
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Unveiling the role of melatonin‐related gene CSNK1D in osteoclastogenesis and its implications for osteoporosis treatment by Jiewen Zhang, Shaobo Wu, Fangze Xing, Ning Kong, Yiwei Zhao, Xudong Duan, Yiyang Li, Kunzheng Wang, Run Tian, Pei Yang

“…Functional enrichment, correlation and protein–protein interaction analyses were conducted. Experimental validation involved in vitro differentiation assays using RAW264.7 cells and in vivo studies with an ovariectomy‐induced rat model of OP to evaluate the role of CSNK1D in osteoclastogenesis to verify its effect on OP. …”
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Malate initiates a proton-sensing pathway essential for pH regulation of inflammation by Yu-jia-nan Chen, Rong-chen Shi, Yuan-cai Xiang, Li Fan, Hong Tang, Gang He, Mei Zhou, Xin-zhe Feng, Jin-dong Tan, Pan Huang, Xiao Ye, Kun Zhao, Wen-yu Fu, Liu-li Li, Xu-ting Bian, Huan Chen, Feng Wang, Teng Wang, Chen-ke Zhang, Bing-hua Zhou, Wan Chen, Tao-tao Liang, Jing-tong Lv, Xia Kang, You-xing Shi, Ellen Kim, Yin-hua Qin, Aubryanna Hettinghouse, Kai-di Wang, Xiang-li Zhao, Ming-yu Yang, Yu-zhen Tang, Hai-long Piao, Lin Guo, Chuan-ju Liu, Hong-ming Miao, Kang-lai Tang

“…Further screening through protein‒protein interaction microarrays identified a L-malate-restrained coupling of BiP with IRF2BP2, a known anti-inflammatory protein. …”
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Aerobic capacity and muscle proteome: Insights from a mouse model by Abel Plaza‐Florido, Alejandro Santos‐Lozano, Susana López‐Ortiz, Beatriz G. Gálvez, Joaquín Arenas, Miguel A. Martín, Pedro L. Valenzuela, Tomàs Pinós, Alejandro Lucia, Carmen Fiuza‐Luces

“…The quadriceps muscle proteome was studied using liquid chromatography with tandem mass spectrometry, with the Search Tool for the Retrieval of Interacting Genes/Proteins database used to generate protein–protein interaction (PPI) networks and enrichment analyses. …”
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Integrated metabolomics and proteomics revealed astragaloside IV inhibiting Pdxk-mediated vitamin B6 metabolism based on liquid chromatography-tandem mass spectrometry combined wit... by Shi Qiu, Sifan Guo, Zhibo Wang, Ying Cai, Dandan Xie, Wanying Sun, Aihua Zhang

“…According to the correlation matrix of the dysregulated metabolites/proteins interactions, we found that Pdxk was ranked as top target signature that was closely related to AA metabolism. …”
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Transcriptome Analysis and Phytohormone Profile Reveal Core Phytohormone Regulating Parthenocarpy in Fingered Citron by Qianbin Chen, Jinjian Xu, Xinjian Zou, Yanjun Zhang, Xiaoxian Zhu, Kewei Zhang, Wenrong Chen, Fanglei Liao, Weidong Guo

“…A total of 66 differentially expressed hormone-related genes were identified, with the auxin pathway emerging as the most prominent in fingered citron. Protein–protein interaction analysis revealed a potential interaction between auxin and abscisic acid (ABA). …”
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Key regions aberrantly connected within cerebello-thalamo-cortical circuit and their genetic mechanism in schizophrenia: an fMRI meta-analysis and transcriptome study by Yarui Wei, Ziyu Wang, Kangkang Xue, Xiaoyu Niu, Longyao Ma, Shaoqiang Han, Baohong Wen, Yong Zhang, Huafu Chen, Jingliang Cheng

“…These genes were specially expressed in the brain tissue, in the neurons of the cerebellum, subcortex and cortex and during nearly all developmental stages, and constructed a protein-protein interaction network supported by 85 hub genes with functional significance. …”
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A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma by Yingkun Xu, Xiunan Li, Yuqing Han, Zilong Wang, Chenglin Han, Ningke Ruan, Jianyi Li, Xiao Yu, Qinghua Xia, Guangzhen Wu

“…Afterward, using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) website, we established the protein-protein interaction (PPI) network of genes related to the PPAR pathway. …”
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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

“…Furthermore, we constructed a protein-protein interaction (PPI) network. In the end, we used quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blotting to measure and compare the expression of Spp1 in patients who accepted percutaneous coronary intervention. …”
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Prediction of potential drug targets and key inhibitors (ZINC67974679, ZINC67982856, and ZINC05668040) against Rickettsia felis using integrated computational approaches by Sudais Rahman, Hsien Liu, Mohibuallah Shah, Mashal M. Almutairi, Iram Liaqat, Tetsuya Tanaka, Chien-Chin Chen, Chien-Chin Chen, Chien-Chin Chen, Chien-Chin Chen, Abdulaziz Alouffi, Abid Ali

“…Through a rigorous screening process and extensive literature review, succinate dehydrogenase emerged as a promising drug target. Protein interaction partners for succinate dehydrogenase were identified using the STRING database. …”
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Identification of Potential Biomarkers and Immune Features of Sepsis Using Bioinformatics Analysis by Fang-Chen Gong, Ran Ji, Yu-Ming Wang, Zhi-Tao Yang, Ying Chen, En-Qiang Mao, Er-Zhen Chen

“…Functional enrichment of the DEGs was analyzed with the DAVID database. Protein-protein interaction networks were derived using the STRING database and visualized using Cytoscape software. …”
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Bioinformatics and Expression Profiling of the DHHC-CRD S-Acyltransferases Reveal Their Roles in Growth and Stress Response in Woodland Strawberry (<i>Fragaria vesca</i>) by Si Gu, Xinghua Nie, Amal George, Kyle Tyler, Yu Xing, Ling Qin, Baoxiu Qi

“…Protein S-acyl transferases (PATs) are a family of enzymes that catalyze protein S-acylation, a post-translational lipid modification involved in protein membrane targeting, trafficking, stability, and protein–protein interaction. S-acylation plays important roles in plant growth, development, and stress responses. …”
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Comprehensive Analysis of Differentially Expressed miRNAs and mRNAs Reveals That miR-181a-5p Plays a Key Role in Diabetic Dermal Fibroblasts by Peng Liu, Yi Zhu, Qin Li, Biao Cheng

“…Subsequently, we constructed the gene correlation network of DEGs to identify hub genes by merging the protein-protein interaction network, weighted gene coexpression network, and predicted miRNA-mRNA regulatory network. …”
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