A Network Pharmacology Study on the Cervix Prescription for Treatment of Cervical Cancer by Yingping Zhu, Liangping Wang, Leilai Xu, Pian Ying

“…We obtained the active ingredients and potential targets in the CP from the literature and the systematic pharmacological analysis platform of traditional Chinese medicine (BATMAN-TCM); the database was used to search for targets related to cervical cancer and to map CP and targets; the core targets were screened, and the protein-protein interaction network (PPI) was constructed using the TCM compound-target network and STRING database. …”
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Bio-primed machine learning to enhance discovery of relevant biomarkers by David M. Henke, Alexander Renwick, Joseph R. Zoeller, Jitendra K. Meena, Nicholas J. Neill, Elizabeth A. Bowling, Kristen L. Meerbrey, Thomas F. Westbrook, Lukas M. Simon

“…Here, we introduce a novel machine learning approach extending the Least Absolute Shrinkage and Selection Operator (LASSO) regression framework to incorporate biological knowledge, such as protein-protein interaction databases, into the regularization process. …”
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MFGE8, ALB, APOB, APOE, SAA1, A2M, and C3 as Novel Biomarkers for Stress Cardiomyopathy by Xiao-Yu Pan, Zai-Wei Zhang

“…Finally, the protein-protein interaction (PPI) network was constructed and Cytoscape was used to find the key genes. …”
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Functional Analysis of Monkeypox and Interrelationship between Monkeypox and COVID-19 by Bioinformatic Analysis by Eun Jung Sohn

“…CytoHubba and Molecular Complex Detection were performed to determine the core genes after a protein–protein interaction (PPI). Metascape/COVID-19 was used to compare DEGs of monkeypox and COVID-19. …”
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Molecular architecture of the altered cortical complexity in autism by Makliya Mamat, Yiyong Chen, Wenwen Shen, Lin Li

“…Cell-specific analyses, protein–protein interaction network analysis and gene temporal expression profiling further elucidated the dynamic molecular landscape associated with these alterations. …”
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MAGEB2-Mediated Degradation of EGR1 Regulates the Proliferation and Apoptosis of Human Spermatogonial Stem Cell Lines by Xueheng Zhao, Zenghui Huang, Yongzhe Chen, Qianyin Zhou, Fang Zhu, Huan Zhang, Dai Zhou

“…Further, using protein interaction prediction, molecular docking, and immunoprecipitation, we found that MAGEB2 interacted with early growth response protein 1 (EGR1) in SSC lines. …”
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Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation by Chia-Chou Wu, Che Lin, Bor-Sen Chen

“…Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. …”
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LC-MS profiling and cytotoxic activity of Angiopteris helferiana against HepG2 cell line: Molecular insight to investigate anticancer agent. by Bipindra Pandey, Shankar Thapa, Mahalakshmi Suresha Biradar, Bhoopendra Singh, Jaya Bahadur Ghale, Pramod Kharel, Prabhat Kumar Jha, Ram Kishor Yadav, Sujan Dawadi, Poojashree V

“…The study design with in-vitro and in-silico technique of the LC-MS followed by a study of the ligand-protein interaction using the molecular docking method, and investigates the cytotoxic activity by MTT assay of A. helferiana bioactive compounds on HepG2 cell lines. …”
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Proteomic Analysis of Exudates from Chronic Ulcer of Diabetic Foot Treated with Scorpion Antimicrobial Peptide by Zhixiang Tan, Zhiguo Yu, Xiaobo Xu, Lanxia Meng, Mosheng Yu, Rui Tao, Yingliang Wu, Zhanyong Zhu

“…In addition, functional annotation, cluster analysis of effects and the analysis of signal pathway, transcription regulation, and protein-protein interaction network were carried out. The results showed that the biochemical changes of wound microenvironment during the treatment involved activated biological functions such as protein synthesis, cell proliferation, differentiation, migration, movement, and survival. …”
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Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas. by Victoria E S Armero, Marie-Pier Tremblay, Andréa Allaire, Simon Boudreault, Camille Martenon-Brodeur, Cyntia Duval, Mathieu Durand, Elvy Lapointe, Philippe Thibault, Maude Tremblay-Létourneau, Jean-Pierre Perreault, Michelle S Scott, Martin Bisaillon

“…Moreover, we show that the expression of Epstein-Barr nuclear antigen 1 (EBNA1) leads to modifications in the AS profile of cellular genes and that the EBNA1 protein interacts with cellular splicing factors. These findings provide insights into the molecular differences between various types of gastric cancer and suggest a role for the EBNA1 protein in the dysregulation of cellular AS.…”
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Identification of key regulators in pancreatic ductal adenocarcinoma using network theoretical approach. by Kankana Bhattacharjee, Aryya Ghosh

“…These DEGs formed the basis for constructing the PDAC protein interaction network, and their network topological properties were calculated. …”
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Identification of Common Oncogenic Genes and Pathways Both in Osteosarcoma and Ewing’s Sarcoma Using Bioinformatics Analysis by Jingwei Zhang, Junchao Huang, Wenjun Liu, Liang Ding, Dongdong Cheng, Haijun Xiao

“…Differentially expressed genes (DEGs) were identified using the limma package. Then, protein-protein interaction (PPI) networks were constructed and hub genes were identified. …”
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Molecular Modeling and Simulation Analysis of Antimicrobial Photodynamic Therapy Potential for Control of COVID-19 by Maryam Pourhajibagher

“…The predicted structure of SARS-CoV-2-SG displayed that it is a protein with a positive charge and random coil dominates other secondary structures located outside the viral cell. The protein-protein interaction network showed that SARS-CoV-2-SG interacted with ten potential interacting partners. …”
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Genome-wide identification and analysis of the NF-Y transcription factor family reveal its potential roles in tobacco (Nicotiana tabacum L.) by Zhen Tian, Luyao Xue, Jincun Fu, Wenting Song, Baojian Wang, Jinhao Sun, Xiujiang Yue, Fanrui Cheng, Jingjing Mao, Jiangtao Chao, Dawei Wang, Shaopeng Li

“…To better understand the genome-wide NF-Y domain-containing proteins, the protein physicochemical properties, chromosomal localization, synteny, phylogenetic relationships, genomic structure, promoter cis-elements, and protein interaction network of NtNF-Ys in tobacco (Nicotiana tabacum L.) were systematically analyzed. …”
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Rapid Identification and Systematic Mechanism of Flavonoids from Potentilla freyniana Bornm. Based on UHPLC-Q-Exactive Orbitrap Mass Spectrometry and Network Pharmacology by Wei Cai, Kailin Li, Shihan Qin, Pei Xiong, Jie Peng, Silin Shi, Zaiqi Zhang

“…Then, the core targets were predicted by protein-protein interaction network and network analysis. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were carried out via DAVID. …”
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Antibody Responses and the Vaccine Efficacy of Recombinant Glycosyltransferase and Nicastrin Against <i>Schistosoma japonicum</i> by Bowen Dong, Haoran Zhong, Danlin Zhu, Luobin Wu, Jinming Wang, Hao Li, Yamei Jin

“…In this study, bioinformatic tools were employed to analyze the structural and functional properties of these proteins, including their signal peptide regions, transmembrane domains, tertiary structures, and protein interaction networks. Recombinant forms of glycosyltransferase and nicastrin were expressed and purified, followed by immunization experiments in BALB/c mice. …”
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Exploring the NANOG-TET2 interaction interface. Effects of a selected mutation and hypothesis on the clinical correlation with anemias by Claudia Testi, Roberta Piacentini, Roberta Piacentini, Alessandro Perrone, Chiara Bartoli, Daniele Leso, Domitilla Pavia, Elisa Pistolesi, Flavio Scipione, Irene Cotronea, Marco Adinolfi Falcone, Marco Ierani, Alberto Boffi, Lorenzo Di Rienzo

“…To address these challenges, we employed an integrated computational approach combining molecular docking, molecular dynamics simulations and protein-protein interaction prediction. Our findings indicate that the single-point mutation might effectively reduce the TET2-NANOG interaction, which would consequently impair cells differentiation and hematopoiesis process, consistent with the clinical presentation of pure red cell aplastic anemia. …”
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PLK3 weakens antioxidant defense and inhibits proliferation of porcine Leydig cells under oxidative stress by Chujie Chen, Jinyan He, Weixian Huang, Dong Xu, Zhaohui Li, Anqi Yang

“…These DEGs were significantly enriched in critical aging pathways, including the p53 signaling pathway, autophagy, and cellular senescence. Protein-protein interaction (PPI) network analysis unveiled 15 key genes related to cell cycle and DNA replication, with polo-like kinase 3 (PLK3) exhibiting increased expression under OS. …”
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Identifying Key Biomarkers and Immune Infiltration in Female Patients with Ischemic Stroke Based on Weighted Gene Co-Expression Network Analysis by Haipeng Xu, Kelin He, Rong Hu, YanZhi Ge, Xinyun Li, Fengjia Ni, Bei Que, Yi Chen, Ruijie Ma

“…Subsequently, we performed functional enrichment analysis and built a protein-protein interaction (PPI) network. Ten genes were selected as the true central genes for further investigation. …”
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Purine-rich element binding protein alpha: a DNA/RNA binding protein with multiple roles in cancers by Shiyi Yu, Chengyang Jiang, Yawen Yang, Fei Cheng, Fangchen Liu, Chang Liu, Xue Gong

“…The oncogenic or tumor-suppressive functions of PURα are realized via regulating RNA/protein interaction, mRNA translation, formation of stress granules (SGs), and transcriptional regulation of several oncogenes and tumor suppressors. …”
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