Network Pharmacology Analysis of the Identification of Phytochemicals and Therapeutic Mechanisms of Paeoniae Radix Alba for the Treatment of Asthma by Jingwei Wang, Ling Peng, Lu Jin, Huiying Fu, Qiyang Shou

“…Cytoscape 3.7.2 was used to determine the target of active ingredients of PRA. Target protein interaction (PPI) network was constructed through the STRING database. …”
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MONet: cancer driver gene identification algorithm based on integrated analysis of multi-omics data and network models by Yingzan Ren, Tiantian Zhang, Jian Liu, Fubin Ma, Jiaxin Chen, Ponian Li, Guodong Xiao, Chuanqi Sun, Yusen Zhang

“…Our method utilizes two graph neural network algorithms on protein-protein interaction (PPI) networks to extract feature vector representations for each gene. …”
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The unconventional Xer recombination machinery of Streptococci/Lactococci. by Pascal Le Bourgeois, Marie Bugarel, Nathalie Campo, Marie-Line Daveran-Mingot, Jessica Labonté, Daniel Lanfranchi, Thomas Lautier, Carine Pagès, Paul Ritzenthaler

“…Moreover, the XerS/dif(SL) recombination requires the streptococcal protein FtsK(SL), probably without the need for direct protein-protein interaction, which we demonstrated to be located at the division septum of Lactococcus lactis. …”
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The Systematic Analysis of Exercise Mechanism in Human Diseases by Lei Pu, Peng Sun

“…After that, we achieved the construction of the protein-protein interaction (PPI) network of DEGs based on the Search Tool for the Retrieval of Interacting Genes online database, and the hub genes were screened and identified. …”
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Identification of genes involved in energy metabolism in preeclampsia and discovery of early biomarkers by Ruohua Li, Cuixia Zhou, Kejun Ye, Haihui Chen, Mengjia Peng

“…Enrichment analyses using gene ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment were performed. Protein-protein interaction networks were constructed to identify key genes, and regulatory networks involving transcription factors, miRNAs, and RNA-binding proteins were established. …”
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Exploration on Molecular Mechanism of Reversal Effect of Compound Danshen Tablets on Hepatic Fibrosis Based on Network Pharmacology by Minling Cao, Jingyue Fan, Xiaoli Yang, Meifeng Shi, Shanshan Lin, Xiaoling Chi

“…Then, the screened target genes were used to construct a protein-protein interaction network. The DAVID enrichment database (the database for annotation, visualization, and integrated discovery) was adopted for GO (Gene Ontology) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment of vital nodes. …”
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Common biomarkers of idiopathic pulmonary fibrosis and systemic sclerosis based on WGCNA and machine learning by Ning Shan, Yu Shang, Yaowu He, Zhe Wen, Shangwei Ning, Hong Chen

“…In this study, weighted correlation network analysis (WGCNA), protein‒protein interaction, Kaplan–Meier curve, univariate Cox analysis and machine learning methods were used on datasets from the Gene Expression Omnibus database. …”
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Differentially Expressed Genes Study Shown Potential for BCG Stimulation in Reducing the Severity of COVID-19 by Irandi Putra Pratomo, Aryo Tedjo, Dimas R Noor, Wisnu Ananta Kusuma

“…The Gene Expression Omnibus (GEO) database was used to select a COVID-19 gene expression data set with GSE164805, GSE14408, and GSE58636, and DEG in each data set were identified using the GEO2R online tools and selected using the adjusted p value (padj) 0.05 criteria. The protein-protein interaction (PPI) network was constructed from DEGs with the same trend of expression (upregulation or downregulation) using STRING version 11. …”
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Identification of Diagnostic Genes and Effective Drugs Associated with Osteoporosis Treatment by Single-Cell RNA-Seq Analysis and Network Pharmacology by Zhanyue Zhang, Tingbao Zhang, Liangshuang Zhou, Jianzhong Guan

“…Key drugs were determined by proteins-proteins interaction and molecular docking. Results. Firstly, 15,577 cells were obtained, and 12 cell subpopulations were identified by clustering, among which 6 cell subpopulations belong to CD45+ BM-MSCs and the other subpopulations were CD45-BM-MSCs. …”
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System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach by Jihua Ran, Hui Li, Huiwu Li

“…In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and follow it to review its biological function. …”
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The Mechanism of Scopolamine’s Effect on Migration Function of Lung Cancer Cells: A Network Pharmacology and Bioinformatics Perspective by Yang Xiao, Mengcong Ma, Qing Gu, Yunfeng Xiao

“…The analysis involved protein-protein interaction (PPI) networks topology analysis to identify these genes, and subsequent differential analysis and survival analysis were conducted using gene expression profile interaction analysis (GEPIA). …”
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Systematic qualitative proteome-wide analysis of lysine malonylation profiling in Platycodon grandiflorus by Qingshan Yang, Shaowei Xu, Weimin Jiang, Fei Meng, Shuting Wang, Zongping Sun, Na Chen, Daiyin Peng, Juan Liu, Shihai Xing

“…Metabolic pathway and protein-protein interaction network analyses suggested these modifications are mainly involved in plant photosynthesis. …”
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Parboiled rice supplementation alleviates high-fat diet-induced hyperlipidemia by regulating genes and gut microbiota in mice by Xiuxiu Wu, Tianyi Guo, Biao Li, Shuai Han, Zuomin Hu, Yi Luo, Dandan Qin, Yaping Zhou, Feijun Luo, Qinlu Lin

“…And 15 differentially expressed genes (DEGs) were validated by quantitative real-time PCR (RT-qPCR), while protein interaction network showed that protein tyrosine phosphatase receptor type C (PTPRC) has a central role. …”
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Integrated Bioinformatics-Based Identification of Potential Diagnostic Biomarkers Associated with Diabetic Foot Ulcer Development by Long Qian, Zhipeng Xia, Ming Zhang, Qiong Han, Die Hu, Sha Qi, Danmou Xing, Yan Chen, Xin Zhao

“…These DEGs were then arranged into a protein-protein interaction (PPI) network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analyses were performed to explore the functional roles of these genes. …”
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Matrix Metalloproteinase-9 is associated with tumor microenvironment remodeling of bladder cancer by Fang Fang, Tiange Wu, Mengxue Wang, Wenchao Li, Zonghao You, Ming Chen, Han Guan

“…Then we used Cox regression to analyze the prognostic value of differentially expressed genes, and the protein–protein interaction network was constructed. Matrix Metalloproteinase-9 (MMP9) was identified as a predictive biomarker related to immune microenvironment. …”
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Structural and Functional Annotation of Hypothetical Proteins of O139 by Md. Saiful Islam, Shah Md. Shahik, Md. Sohel, Noman I. A. Patwary, Md. Anayet Hasan

“…Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. …”
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Characteristics of transcriptome and chromatin accessibility in the peripheral blood after acute hypoxia exposure by Kuo Zeng, Pei-ru Yuan, Jin-feng Xuan, Lai-xi Zhao, Xiao-na Li, Jun Yao, Dong Zhao

“…Moreover, the combined analysis of RNA-seq and ATAC-seq revealed that 10 hub genes were independently identified from the protein–protein interaction (PPI) network for each altitude. Gene enrichment analysis displayed that most hub genes were related with hypoxia pathways. …”
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LASSO–MOGAT: a multi-omics graph attention framework for cancer classification by Fadi Alharbi, Aleksandar Vakanski, Murtada K. Elbashir, Mohanad Mohammed

“…By utilizing differential expression analysis (DEG) with Linear Models for Microarray (LIMMA) and LASSO regression for feature selection and leveraging graph attention networks (GATs) to incorporate protein–protein interaction (PPI) networks, LASSO–MOGAT effectively captures intricate relationships within multi-omics data. …”
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Identification of Functional Modules and Key Pathways Associated with Innervation in Graft Bone—CGRP Regulates the Differentiation of Bone Marrow Mesenchymal Stem Cells via p38 MAP... by Ziqian Wu, Xudong Wang, Jingcun Shi, Anand Gupta, Yuhan Zhang, Bingqing Zhang, Yang Cao, Lei Wang

“…In parallel, we established protein–protein interaction networks to screen functional modules. …”
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Monosaccharide coatings on nanoparticles affect protein corona formation but not the interaction with their binding receptor by Eva Clemente, Ruth Mateu, Avelino Ferreira, Tanja Ludtke, Tanja Ludtke, Hender Lopez, Sergio E. Moya, Luigi Lay, Mahmoud G. Soliman, Marco P. Monopoli

“…Our findings show that the glycan-coated NPs exhibit stabilisation after protein interaction, with Man coatings showing the lowest protein affinity and that the glycans are biologically active and capable of binding to glycan receptors (such as Concanavalin A) despite the presence of a complex protein environment. …”
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