Identification of hub genes and pathogenesis in Kawasaki disease based on bioinformatics analysis by Min Cao, Zhenhu Zhang, Qian Liu, Yuda Zhang

“…Materials and Methods: Gene Expression Omnibus (GEO) datasets GSE68004 and GSE73461 were downloaded, and the differentially expressed genes (DGEs) were taken, along with DEGs enrichment analysis and protein interaction network. Finally, five algorithms in CytoHubba plug-in were applied to obtain hub genes. …”
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Exosomal insights into ovarian cancer stem cells: revealing the molecular hubs by Kiana Sojoudi, Maryam Solaimani, Hossein Azizi

“…In this study, we used a protein-protein interaction (PPI) network. Using the Clustermaker2 app and the MCODE algorithm, we identified six significant clusters within the network, highlighting regions involved in functional pathways. …”
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DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features by Omar Barukab, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou

“…It is DNA, which makes a living thing, a living thing. Protein interaction with DNA performs an essential role in regulating DNA functions such as DNA repair, transcription, and regulation. …”
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Exploring effector protein dynamics and natural fungicidal potential in rice blast pathogen Magnaporthe oryzae. by Jannatul Ferdousy, Tanjin Barketullah Robin, Mst Sanjida Nasrin, Istiak Ahmed, Tawsif Hossain, Md Mehedi Hasan, Mehrab Hassan Soaeb, Md Ahsanul Tamim, Nusrat Jahan Yeasmin, Ummay Habiba, Nadim Ahmed, Nurul Amin Rani, Md Shishir Bhuyian, Suvarna N Vakare, Abu Tayab Moin, Rajesh B Patil, Mohammad Shahadat Hossain

“…Genetic and genomic studies have identified key genes and proteins, such as AvrPik variants and MAX proteins, that are crucial for the pathogen's virulence. These effector proteins interact with specific alleles of the Pik gene family on rice chromosome 11, modulating the host's immune response. …”
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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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Identification of Differentially Expressed Genes in Pituitary Adenomas by Integrating Analysis of Microarray Data by Peng Zhao, Wei Hu, Hongyun Wang, Shengyuan Yu, Chuzhong Li, Jiwei Bai, Songbai Gui, Yazhuo Zhang

“…Gene function analysis including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) networks analysis was conducted to interpret the biological role of those DEGs. …”
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Identification and Expression Profiling of the BTB Domain-Containing Protein Gene Family in the Silkworm, Bombyx mori by Daojun Cheng, Wenliang Qian, Meng Meng, Yonghu Wang, Jian Peng, Qingyou Xia

“…The BTB domain is a conserved protein-protein interaction motif. In this study, we identified 56 BTB domain-containing protein genes in the silkworm, in addition to 46 in the honey bee, 55 in the red flour beetle, and 53 in the monarch butterfly. …”
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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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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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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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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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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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