Mechanism of Radix Bupleuri and Hedysarum Multijugum Maxim drug pairs on liver fibrosis based on network pharmacology, bioinformatics and molecular dynamics simulation. by Lefei Yu, Pan Yu, Yongchang Cao, Weiya Cao

“…In the protein-protein interaction (PPI) network, the top 10 hub targets with the highest node connection values were TNF, IL-6, AKT1, EGFR, HIF1A, PPARG, CASP3, SRC, MMP9 and HSP90AA1. …”
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Molecular subtype of gastric cancer based on apoptosis-related genes reveals differential immune microenvironment and intratumoral microorganisms distribution by Xuan Yu, Yongfu Shao, Haotian Dong, Jianing Yan, Xinjun Zhang, Guoliang Ye

“…Subsequently, significant differences were found in the tumor immune microenvironment, intratumoral microorganisms, gene expression, signaling pathways, and protein interaction networks between the two subtypes. GPX3, PLAT, and CAV1 were identified as key prognostic genes related to apoptosis in GC, with a focus on their impact on disease progression-related pathways. …”
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Exploring the Mechanism of Antioxidant Action of Bitter Almond Based on Network Pharmacology and Molecular Docking Techniques by Xuehua Feng, Jingya Niu, Zurong Song, Ali Tao, Rumin Zong, Wenqing Pei, Panpan Gong

“…The active ingredients of bitter almond were obtained through the traditional Chinese medicine systematic pharmacology database and analysis platform (TCMSP), and the main active ingredients were screened by bioavailability (OB) and drug-like properties (DL); the GeneCards database was used to search antioxidant-related disease targets through the traditional Chinese medicine systematic pharmacology database and analysis; building a “drug-disease-target” visual network map with Cytoscape 3.9.0 software; a protein interaction (PPI) network was constructed using STRING website and core targets were screened; GO function and KEGG pathway enrichment analysis were obtained using Metoscape. …”
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Identification of Potential Abnormal Methylation-Modified Genes in Coronary Artery Ectasia by Xiuchun Yang, Yijun Zong, Zhentian Zhang, Yan Zhao, Xueying Gao, Jie Zhang, Qian Hou, Renyi Li, Bing Xiao

“…Finally, after taking interaction genes between DEGs and DMGs, abnormal methylation-modified genes were identified, followed by protein–protein interaction analysis and expression validation using reverse transcriptase polymerase chain reaction. …”
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Fracture-healing effects of Rhizoma Musae ethanolic extract: An integrated study using UHPLC-Q-Exactive-MS/MS, network pharmacology, and molecular docking. by Jian Zhang, Wanyan Shen, Fanzhi Liu, Hehe He, Shuquan Han, Lina Luo

“…Topological analysis of the protein-protein interaction (PPI) network identified 59 core targets, including key proteins like AKT1, IL-6, and EGFR, known for their anti-inflammatory properties and ability to enhance bone cell proliferation and differentiation. …”
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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

“…Besides, a protein-protein interaction (PPI) network of DEFRGs was constructed by STRING database. …”
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Use of Graph Database for the Integration of Heterogeneous Biological Data by Byoung-Ha Yoon, Seon-Kyu Kim, Seon-Young Kim

“…We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. …”
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Gene Expression Profiling of the Sciatic Nerve in Streptozotocin-Induced Diabetic Rats with Peripheral Neuropathy by Yiji Tu, Zenggan Chen, Feng Zhang, Zhenglin Di, Junhui Zhang, Li Cai

“…DEGs from the 3 most highly connected clusters in the protein-protein interaction network were enriched for biological processes or pathways such as “cell division,” “cell cycle,” “protein phosphorylation,” “chemokine signaling pathway,” “neuropeptide signaling pathway,” “response to drug,” “cellular response to insulin stimulus,” “PPAR signaling pathway,” and “glycerophospholipid metabolism.” …”
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Comprehensive analysis pinpoints CCNA2 as a prognostic and immunological biomarker in non-small cell lung cancer by Liming Zhang, Shaoqiang Wang, Lina Wang

“…Using STRING, we constructed a protein-protein interaction (PPI) network to pinpoint hub genes. …”
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Bioinformatics Analysis of Genes and Mechanisms in Postherpetic Neuralgia by Yong Qiu, Meng-Lei Hao, Xu-Tao Cheng, Zhen Hua

“…Differentially expressed genes (DEGs) were identified and analyzed by Gene Ontology. Protein-protein interaction (PPI) network was constructed. The miRNA associated with neuropathic pain and inflammation was found in miRNet. …”
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Exploring the mechanism of Schisandra rubriflora in the treatment of polycystic ovary syndrome based on network pharmacology and molecular docking by Zhengyan Dou, Qingxian Li, Jing Zhang, Xin Zhang

“…Differentially expressed genes (DEGs) associated with PCOS were obtained by analyzing GSE54248 dataset. A protein-protein interaction network was constructed, and topological analyses were performed to identify the hub targets and main bioactive components. …”
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Excessive Weight Gain During Pregnancy Increased Ponoxarase 1 Level in Neonatal Cord Blood by Serhat Ege, Hasan Akduman, Ayşegül Aşır, Tuğcan Korak

“…Umbilical cord blood samples were collected immediately post-delivery and analyzed for serum oxidative stress markers (total oxidant status (TOS), total antioxidant status (TAS), paraoxanase (PON), aryl esterase, thiol, and catalase activities). Protein interaction networks were generated using Cytoscape (v3.10.3), and the overlapping proteins were further analyzed for functional annotations with ShinyGO (0.80). …”
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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

“…Then mitochondria-associated DEGs (MitoDEGs) were obtained. Protein-protein interaction (PPI) networks were constructed to identify central MitoDEGs that are strongly associated with MI. …”
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Identification and mechanistic insights of cell senescence-related genes in psoriasis by Guiyan Deng, Cheng Xu, Dunchang Mo

“…The intersection of DEGs with cell senescence-related genes from the CellAge database was used to identify the candidate genes. Protein-protein interaction networks, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the functions and pathways of these genes. …”
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Contact-dependent growth inhibition (CDI) systems deploy a large family of polymorphic ionophoric toxins for inter-bacterial competition. by Tiffany M Halvorsen, Kaitlin A Schroeder, Allison M Jones, Disa Hammarlöf, David A Low, Sanna Koskiniemi, Christopher S Hayes

“…The specificity of this protein interaction network provides a mechanism for self/nonself discrimination between E. coli isolates.…”
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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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Network analyses of brain tumor multiomic data reveal pharmacological opportunities to alter cell state transitions by Brandon Bumbaca, Jonah R. Huggins, Marc R. Birtwistle, James M. Gallo

“…By incorporating phosphoproteomic measurements from the same patients, a protein–protein interaction network (PPIN) was constructed for each cell state. …”
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The immune-related gene CD5 is a prognostic biomarker associated with the tumor microenvironment of breast cancer by Yi Zhao, Hengheng Zhang, Wenwen Wang, Guoshuang Shen, Miaozhou Wang, Zhen Liu, Jiuda Zhao, Jinming Li

“…Univariate Cox regression analysis of overall survival was performed on the DEGs, and a protein–protein interaction network of their protein products was generated. …”
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Bioinformatics combining machine learning and single-cell sequencing analysis to identify common mechanisms and biomarkers of rheumatoid arthritis and ischemic heart failure by Ziyi Sun, Jianguo Lin, Xiaoning Sun, Zhangjun Yun, Xiaoxiao Zhang, Siyu Xu, Jinlong Duan, Kuiwu Yao

“…Five hub genes (CD2, CD3D, CCL5, IL7R, and SPATA18) were identified through protein-protein interaction (PPI) network analysis and machine learning. …”
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Mendelian randomization and multiomics comprehensively reveal the causal relationship and potential mechanism between atrial fibrillation and gastric cancer by Zhao Sicheng, Zhao Sicheng, Zhang Jingcheng, Zhang Jingcheng, Zhang Shuo, Zhang Shuo, Lou Jiaheng, Lou Jiaheng, Cai Yan, Cai Yan, Bai Xing, Bai Xing, Jiang Tao, Jiang Tao, Jiang Tao, Zhang Guangji, Zhang Guangji, Zhang Guangji

“…Subsequently, analysis identifies 62 AF-GC co-associated genes and constructs a protein-protein interaction network of key genes. High-throughput sequencing data were further used to analyze the association between the two and their impact on the survival outcome of gastric cancer.ResultsThe results showed that AF was negatively associated with gastric cancer, and further analysis revealed that this relationship was independent of GC risk factors such as chronic gastritis, Helicobacter pylori infection, and alcohol consumption. …”
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