Drp1–associated genes implicated in sepsis survival by Marissa D. Pokharel, Marissa D. Pokharel, Anlin Feng, Anlin Feng, Ying Liang, Ying Liang, Wenli Ma, Wenli Ma, Saurabh Aggarwal, Hoshang Unwalla, Stephen M. Black, Stephen M. Black, Stephen M. Black, Ting Wang, Ting Wang, Ting Wang

“…Next, we compared genes of proteins that interact with Drp1 to sepsis survival genes and identified 7 common genes, establishing a GS we term as protein-protein interaction (PPI)-based GS. To evaluate if these GSs can predict sepsis survival, we used publicly available human blood transcriptomic datasets from sepsis patients. …”
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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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Investigating the Pulmonary Host Response of <i>Acinetobacter baumannii</i> Infection-Associated Pneumonia by Metagenomic Next-Generation Sequencing by Mu-Jung Chou, Chih-Hung Cheng, Hui-Ching Wang, Ming-Ju Tsai, Chau-Chyun Sheu, Wei-An Chang

“…The STRING was employed for identifying protein interaction pathways related to the pulmonary host response to pneumonia caused by <i>A. baumannii</i> without antimicrobial-resistant genes. …”
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Transcriptomic analysis of melatonin on the mechanism of embryonic gonadal development in female Jilin white geese by Jin Yu, Ichraf Mabrouk, Qiuyuan Liu, Yuxuan Zhou, Yupu Song, Jingyun Ma, Fengshuo Liu, Xiangman Hu, Zhiyi Yang, Yuxia Zeng, Jingtao Hu, Yongfeng Sun

“…These DEGs were enriched in Gene Ontology (GO) terms related to the microtubule cytoskeleton, cytoskeleton, cell adhesion, and biological adhesion and the KEGG enrichment analysis suggested that the DEGs were mainly enriched in “MAPK signaling pathway”, “Wnt signaling pathway”, “Calcium signaling pathway”, “Focal adhesion”, “Neuroactive ligand-receptor interaction”, “Melanogenesis”, “mTOR signaling pathway”, “ECM-receptor interaction”, and “TGF-beta signaling pathway” in the two comparison groups. The protein-protein interaction network analysis (PPI) indicated that selected DEGs, such as PDIA3, ATCB, PKM, PGAM1, NME2, LDHB, and CALM2, were highly related to the regulation of the reproduction system development. …”
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A Network Pharmacology-Based Strategy for Unveiling the Mechanisms of Tripterygium Wilfordii Hook F against Diabetic Kidney Disease by Yuyang Wang, Tongtong Liu, Fang Ma, Xiaoguang Lu, Huimin Mao, Weie Zhou, Liping Yang, Ping Li, Yongli Zhan

“…Then, we obtained DKD targets from GeneCards and OMIM and collected and analyzed TwHF-DKD common targets using the STRING database. Protein-protein interaction (PPI) network was established by Cytoscape and analyzed by MCODE plugin to get clusters. …”
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Based on bioinformatics, SESN2 negatively regulates ferroptosis induced by ischemia reperfusion via the System Xc−/GPX4 pathway by Jiejie Hu, Lijun Qin, Guoqiang Zhu, Jingjing Ren, Hongxia Wang, Jing Jin, Haixue Zheng, Dan Li, Zhaoming Ge

“…Differentially expressed gene (DEG) enrichment analysis highlighted ferroptosis-related pathways.ResultsUsing Venn analysis, nine ferroptosis-related DEGs were identified, namely, Slc3a2, Slc7a11, Ccn2, Tfrc, Atf3, Chac1, Gch1, Lcn2, and Sesn2. Protein–protein interaction (PPI) analysis combined with molecular complex detection (MCODE) identified six hub genes, namely, Ddit3, Atf3, Sesn2, Trib3, Ppp1r15a, and Gadd45a. …”
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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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The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research by Ashkan Kalantary-Charvadeh, Saman Morovat, Somayeh Aslani, Nasrin Ziamajidi, Amirnader Emami Razavi, Roghayeh Abbasalipourkabir

“…Afterward, protein-protein interaction network and functional enrichment analyses disclosed the biological activity of target genes. …”
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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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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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Potential role of P4HB in the tumor microenvironment and its clinical prognostic value: a comprehensive pan-cancer analysis and experimental validation with a focus on KIRC by Linxue Zhang, Yu-wei Li, Tianyi Xie, Ke Sun, Xiang Huang, Wei Xiong, Rui-ji Liu

“…In addition, we used the Metascape database to construct protein–protein interaction networks and the single-cell Sequencing database for functional analysis. …”
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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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Identification of Crucial lncRNAs for Luminal A Breast Cancer through RNA Sequencing by Xinjian Jia, Hai Lei, Xuemei Jiang, Ying Yi, Xue Luo, Junyan Li, Yu Chen, Sha Liu, Chengcheng Yang

“…RNA sequencing was performed to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in luminal A breast cancer. The protein-protein interaction (PPI), DElncRNA-DEmRNA coexpression, DElncRNA-nearby DEmRNA interaction networks, and functional annotation were performed to uncover the function of DEmRNAs. …”
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