Identification of Critical Signature in Post‐Traumatic Stress Disorder Using Bioinformatics Analysis and in Vitro Analyses by Lifen Liu, Yang Liu, Rui Li, Yue Teng, Shuyang Zhao, Jinhong Chen, Changjiang Li, Xinyu Hu, Lin Sun

“…The MCODE plugin in Cytoscape software was utilized to analyze the protein–protein interaction (PPI) network. Anxiety and depression in a mice stress model were assessed using the open‐field test (OFT), elevated plus maze test (EPMT), and forced swimming test (FST). …”
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Deciphering the role of miRNA-mRNA interactions in cerebral vasospasm post intracranial hemorrhage by Xiang Chu, Xiang Chu, Xiyan Zhu, Honghao Xu, Wenbing Zhao, Debin Guo, Xing Chen, Jinze Wu, Lei Li, Hao Wang, Jun Fei

“…By employing the degree scores method for each gene, we identified the top 10 genes and developed a protein-protein interaction (PPI) network. Additionally, we discovered 19 DEMs associated with CVS and integrated them with mRNA dataset analysis to construct a miRNA-mRNA network, which comprised 8 functionally differentially expressed DEMs and 6 target mRNAs. …”
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Identification of a transcription factor AoMsn2 of the Hog1 signaling pathway contributes to fungal growth, development and pathogenicity in Arthrobotrys oligospora by Qianqian Liu, Kexin Jiang, Shipeng Duan, Na Zhao, Yanmei Shen, Lirong Zhu, Ke-Qin Zhang, Jinkui Yang

“…Furtherly, we analyzed the protein interaction network of AoMsn2 based on the Kyoto Encyclopedia of Genes and Genomes pathway map and the online website STRING. …”
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Therapeutic target genes and regulatory networks of gallic acid in cervical cancer by Zhixi You, Ye Lei, Yongkang Yang, Zhihui Zhou, Xu Chao, Keyi Ju, Songyi Wang, Yuanyuan Li, Yuanyuan Li

“…Subsequently, the function enrichment analysis and protein–protein interaction of the DEGs were conducted. The candidate genes were identified using the Cytoscape software Gentiscape2.2 and MCODE plug-ins. …”
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Determining the mechanism of Shuxuening injection against liver cirrhosis through network pharmacology and animal experiments by Qiyao Liu, Tingyu Zhang, Yongan Ye, Xin Sun, Huan Xia, Xu Cao, Xiaoke Li, Wenying Qi, Yue Chen, Xiaobin Zao

“…Methods: Target genes of SXN and LC were retrieved from public databases, and enrichment analysis was performed. A protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), and hub genes were identified using Molecular Complex Detection (MCODE). …”
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Integrated bioinformatics analysis of the effects of chronic pain on patients with spinal cord injury by Jinlong Zhang, Jinlong Zhang, Longju Qi, Yuyu Sun, Yuyu Sun, Shiyuan Chen, Jinyi Liu, Jiaxi Chen, Fangsu Yan, Wenqi Wang, Qinghua Wang, Liang Chen

“…Additionally, we conducted an in-depth examination of immune infiltration in SCI to elucidate its correlation with chronic pain.ResultsAnalyzing 101 DEGs associated with SCI and chronic pain, we constructed a protein interaction network and identified 15 hub genes. …”
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Spatially resolved transcriptomics reveals gene expression characteristics in uveal melanoma by Jing-Ying Xiu, Yu-Ning Chen, Ya-Li Mao, Jing-Ting Luo, Hao-Wen Li, Yang Li, Wen-Bin Wei

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes, Genomes (KEGG) functional enrichment analysis, and protein–protein interaction (PPI) network were performed to define the biological function of each cluster. …”
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Identification and validation of diagnostic genes IFI44 and IRF9 in insomnia-associated autoimmune uveitis by Chao Wu, Hui Feng, Meng Tian, Baorui Chu, Xianyang Liu, Shuhao Zeng, Yakun Wang, Hong Wang, Shengping Hou, Qingfeng Liang

“…Weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI), functional enrichment, and CMap analyses were then performed to identify pathogenic genes, underlying mechanisms, and potential therapeutic drugs for insomnia-associated AU. …”
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SHP2 is essential for the progesterone-promoted proliferation and migration in breast cancer cell lines by Hui-Chen Wang, Hui-Chen Wang, Wen-Sen Lee, Wen-Sen Lee, Wen-Sen Lee, Wen-Sen Lee

“…Immunoprecipitation assay and Western blot analysis were performed to evaluate protein-protein interaction and protein expression, respectively. …”
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Identification and verification of autophagy-related gene signatures and their association with immune infiltration and drug responsiveness in epilepsy by Han-han He, Xiao-ge Zhang, Fen-fang Chen

“…Subsequently, protein–protein interaction, transcription factors and miRNAs networks were constructed. …”
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HLA-DMB correlates with antitumor immunity and an improved prognosis in endometrial carcinoma tumors by Xiaoyu Xi, Xiaona Zhang, Jianxin Tang, Xiumei Fan, Jiexian Du

“…Univariate COX regression analysis was performed to identify prognostic factors for endometrial carcinoma (EC), and a multivariate COX proportional hazards regression model was used to confirm that HLA-DMB can serve as an independent prognostic factor for EC. The protein interaction network of HLA-DMB was constructed using the STRING database, and the chemical drugs related to HLA-DMB were predicted through the CTD database. …”
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Analysis of the mechanism of Zangjiangzhi capsule in the treatment of hyperlipidemia based on its ingredients identified by UHPLC-Q-Exactive-Orbitrap-MS by Changting He, Yuling Zhao, Yongchun Huang, Yudong Su, Shoude Zhang

“…The SwissTargetPrediction database was used to predict compound targets, and GeneCards, DisGeNet, OMIM, and DRUGBANK databases were used to identify HLP-related targets. Protein–protein interaction diagrams were constructed using the STRING database. …”
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Exploring and Verifying the Mechanism and Targets of Shenqi Pill in the Treatment of Nonalcoholic Steatohepatitis via Network Pharmacology and Experiments by Beihui He, Zheng Chen, Yunmeng Nie, Minmin Luo, Sumei Xu, Junbin Yan, Zhiyun Chen

“…Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein–protein interaction (PPI) analysis were used to search for crucial target genes and mechanisms. …”
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Exploring the inhibitory effect and mechanism of isorhamnetin therapy on oral squamous cell carcinoma based on network pharmacology and molecular docking by YU Fangfang, ZHOU Jingjing, YANG Jie, QU Huijuan, HUI Guangyan

“…Methods The key targets were obtained by constructing the PPI protein interaction network based on the common intersection targets of Iso-OSCC. …”
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Potential Value of Circular RNA circTBC1D4 in Gastrointestinal Stromal Tumors by null Chunyan-Zou, null Yanpeng-He, null Changshun-Xie, null Fulai-Gao, null Xiaoli-Xie, null Xiukun-Chai, null Chenxi-He, null Dongqiang-Zhao

“…The hub genes of protein-protein interaction (PPI) network and cytoHubba were also defined. …”
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Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma by Rui Mu, Yuehong Shen, Chuanbin Guo, Xinyun Zhang, Hongyu Yang, Huijun Yang

“…The signature was also evaluated based on clinical variables, predictive nomogram, mutation analysis, infiltrating immune cells, immune-related pathways, and chemotherapeutic efficacy. The protein-protein interaction (PPI) network and functional enrichment pathway investigations were utilized to explore possible potential molecular mechanisms. …”
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Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer’s disease by Waimao Gao, Guang Yang, Xinjuan Liu, Kaifan Hu, Jie Pan, Xingyu Wang, Yan Zhao, Ying Xu

“…Then we performed Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses on these common targets. The protein-protein interaction (PPI) network was constructed and clusters were obtained using the Molecular Complex Detection (MCODE) and the Cytohubba plugins. …”
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Identification of core biomarkers for tuberculosis progression through bioinformatics analysis and in vitro research by Zhanpeng Chen, Qiong Wang, Quan Ma, Jinyun Chen, Xingxing Kong, Yuqin Zeng, Lanlan Liu, Shuihua Lu, Xiaomin Wang

“…Subsequent Protein-protein interaction (PPI) analysis and Receiver Operating Characteristic (ROC) curve analysis identified four core genes closely associated with TB progression, namely Rac Family Small GTPase 1 (RAC1), Ring-Box 1 (RBX1), Mitochondrial Ribosomal Protein L33 (MRPL33), and ELAV Like RNA Binding Protein 1 (ELAVL1). …”
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Microbiota governs host chenodeoxycholic acid glucuronidation to ameliorate bile acid disorder induced diarrhea by Zishen Lin, Yue Feng, Jinping Wang, Zhaoyue Men, Xi Ma

“…LKB1 binds with P53 based on protein interaction, ultimately resists to apoptosis and diarrhea. …”
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Construction of a circRNA-miRNA-mRNA Regulatory Network for Coronary Artery Disease by Bioinformatics Analysis by Zebo Zhang, Haiyan Qian, Li Wang, Zhenbo Tao, Keai Cheng, Kaiyue Wang, Yanqing Xie, Lina Zhang

“…Bioinformatics analysis was performed to construct a ceRNA regulatory network, from which the hub genes involved were identified through protein-protein interaction (PPI) networks leading to the identification of the circRNA-miRNA-hub gene subnetwork. …”
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