Characterization of gene expression profiles in Alzheimer's disease and osteoarthritis: A bioinformatics study. by Nian Liu, Qian Deng, Zining Peng, Danning Mao, Yuanbo Huang, Fanyu Meng, Xiaoyu Zhang, Jiayan Shen, Zhaofu Li, Weitian Yan, Jiangyun Peng

“…Subsequently, the Co-DEGs were enriched, and a protein-protein interaction network was constructed to identify core genes. …”
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Network pharmacology combined with experimental verification for exploring the potential mechanism of phellodendrine against depression by Lili Hu, Na Wu, Jue Wang, Donghui Cai

“…The intersection targets between PHE and MDD were obtained to identify as targets for PHE against MDD, followed by protein–protein interaction network, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. …”
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Identified VCAM1 as prognostic gene in gastric cancer by co-expression network analysis by Wenjuan Li, Hong Gao, Jianjun Liu

“…Co‐expression gene modules were constructed via Weighted Gene Co‐Expression Network Analysis (WGCNA), followed by deciphering gene functions and protein–protein interaction networks within significantly associated modules. …”
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Binding Investigation of Some Important Metal Ions Copper (I), Nickel (II), and Aluminium (III) with Bovine Serum Albumin Using Valid Spectroscopic Techniques by Hassan A. Alhazmi, Md Shamsher Alam, Mohammed Albratty, Asim Najmi, Ahmed A. Abdulhaq, Rym Hassani, Waquar Ahsan, Abdulrahman N. Qramish

“…Therefore, it can be inferred that the FT-IR and UV techniques might be utilised effectively to assess the metal-protein interaction and can have wide application in routine analysis. …”
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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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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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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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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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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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Genome-wide characterization of the MADS-box gene family in Paeonia ostii and expression analysis of genes related to floral organ development by Xueting Yang, Qi Guo, Shaodan Liu, Duoduo Wang, Dingding Zuo, Tongfei Niu, Dongfeng Wei, Lili Guo, Xiaogai Hou

“…We additionally created protein‒protein interaction networks for PoMADS proteins and analysed proteins that could interact among PoMADSs in Arabidopsis thaliana and grape. …”
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