Glucometabolic-Related Genes as Diagnostic Biomarkers and Therapeutic Targets for Alzheimer’s Disease and Type 2 Diabetes Mellitus: A Bioinformatics Analysis by Shuo Liu, He Chen, Xiao-Dong He, Xiao-Ou Yang

“…A range of bioinformatics tools were employed for functional annotation, pathway enrichment, protein interaction network construction, module analysis, ROC curve assessment, correlation matrix construction, gene set enrichment analysis, and gene-drug interaction mapping of these DEGs. …”
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GPX3 as a Novel and Potential Therapeutic Target in the Shared Molecular Mechanisms of Traumatic Brain Injury and Parkinson’s Disease by Wang Y, Fang J, Yuan Q, Yu J, Hu J

“…Further analyses, including GO and KEGG pathway enrichment, protein-protein interaction (PPI) network construction, hub gene identification, as well as miRNA and transcription factor prediction and drug candidate screening, were conducted. …”
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Molecular Characterization and Clinical Characteristics of m5C-Based RNA Methylation in Spinal Cord Injury: Validated by qPCR by Liang Cao, Wen Jun Pi, Qiang Zhang, Qing Li

“…Through the creation of a protein–protein interaction network, we screened 11 hub genes. We demonstrated their importance between SCI group and sham group using real-time reverse transcription-quantitative polymerase chain reaction in rat model. …”
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A Network Pharmacology-Based Approach for Exploring Key Active Compounds and Pharmacological Mechanisms of Tangshen Formula for Treatment of Diabetic Nephropathy by Weie Zhou, Xuefeng Zhou, Yuan Zhang, Yuyang Wang, Wenjie Wu, Haojun Zhang, Tingting Zhao, Liang Peng, Hailing Zhao, Ping Li

“…A network pharmacology approach was firstly applied to explore multiple active compounds and multiple key pharmacological mechanisms for TSF treating DN by drug-targeted interaction databases, herb-compound-target network, protein-protein interaction network, compound-target-pathway network, and analysis methods. …”
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Linking evidence for targeted blood biomarkers in post-stroke cognitive impairment and dementia by Jinny Hong, Katherine Mun, Katherine Mun, Kyle C. Kern, Kyle C. Kern, Marissa Thirion, Jason D. Hinman, Jason D. Hinman

“…In addition to this comprehensive review, we performed a protein-protein network analysis of the putative blood biomarkers for PSCID and (surprisingly) find they exist in a highly connected protein-protein interaction network centered on inflammatory and neurodegenerative biomarkers suggesting shared biology underlies the pathogenesis of PSCID. …”
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Identification and characterization of interacting proteins of transcription factor DpWRI1-like related to lipid biosynthesis from microalga Dunaliella parva by Lingru Ruan, Limei Huang, Lina Wu, Jinghui Gu, Yanyan Liang, Xiuli Liang, Changhua Shang

“…Yeast two-hybrid was widely used to identify protein-protein interaction. In this study, the interacting proteins of DpWRI1-like were obtained using yeast two-hybrid technique to further realize the role of DpWRI1-like. …”
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Identification and functional analysis of hub genes involved in deoxynivalenol-induced enterotoxicity in porcine (Sus scrofa) by Jinhua He, Geng Zhao, Mingxia Chen, Ximing Ren, Peizhi Zhu, Zhizhong Liu, Jiayi Zhou, Hanwei Chen, Chuqiao Xiao, Xiang-Guang Li

“…Then, genes in the highest co-expressed module were intersected with the up-regulated DEGs to construct a Protein-Protein Interaction network, resulting in 237 overlapping genes. …”
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Nox1/PAK1 is required for angiotensin II-induced vascular inflammation and abdominal aortic aneurysm formation by Hui He, Tianyu Jiang, Meng Ding, Yuan Zhu, Xiaoting Xu, Yashuang Huang, Wenfeng Yu, Hailong Ou

“…Further, we found the Nox1 protein interacted with p21-activated kinase 1 (PAK1) in Ang II-stimulated VSMCs. …”
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Exploring the multi-targeted mechanism of Saikosaponin A in prostate cancer treatment: a network pharmacology and molecular docking approach by Genbao Zhu, Genbao Zhu, Genbao Zhu, Zhiming Jiang, Niuping Zhu, Niuping Zhu, Donghui Wang, Donghui Wang, Tianpeng Guo, Tianpeng Guo, Yiqing Meng, Yiqing Meng, Yi Zhu, Yi Zhu, Kemeng Tan, Mengxue Hu, Heng Tang, Xuannian Wang, Xuannian Wang

“…However, the mechanism underlying the effects of SSA in prostate cancer treatment remains elusive.MethodsIn this study, a network pharmacology approach was applied to identify relevant targets from drug- and disease-related databases, and intersections were analyzed using Venny2.1 to construct a Protein-Protein interaction (PPI) interaction network. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to elucidate associated biological functions and signaling pathways. …”
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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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Abnormal ac4C modification in metabolic dysfunction associated steatotic liver cells by Xiqian Zhang, Yaxian Zheng, Jing Yang, Yan Yang, Qin He, Min Xu, Fangyi Long, Yujie Yang

“…Among these proteins, JUN, caveolin-1 (CAV1), fatty acid synthase (FASN), and heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) were identified as core proteins through protein–protein interaction (PPI) network analysis using cytoscape software. …”
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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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Collagen prolyl 4-hydroxylase subunit α member-induced head and neck squamous cell carcinoma aggressiveness is antagonized by LLGL2 via redu... by Xu Miao, Shi Run, Yang Jie, Chen Heng, Liu Shihua, Yu Shupei, Li Sasa, He Wenqiang, Sy Man-Sun, Lu Mingjian, Zhang Huixia, Li Chaoyang

“…By constructing a functional protein interaction network of <sc>C-P4HAs</sc> and analyzing molecules whose expressions are correlated significantly with that of C-P4HAs, we identify scribble cell polarity complex component 2 (LLGL2) as a factor that antagonizes the effects of overexpressed <sc>C-P4HAs</sc> on HNSC. …”
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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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Qinggan Yipi capsule ameliorates hepatic fibrosis in rats by down-regulating the TGF-β1/Smad2/3 signaling pathway and improving gut microbiota imbalance by Wenjing Xue, Haiqing Liu, Ziheng Su, Siqi Wang, Junping Cheng, Yunzhi Pan, Lurong Zhang

“…The composition of the gut microbiota was analyzed using 16S rRNA gene sequencing.ResultsHistopathological analysis, serum biochemical tests, and ELISA measurements showed that QgYp effectively decreased the levels of ALT, AST, HA, LN, PCIII, and IV-C while improving collagen deposition and hepatocyte necrosis. Protein-protein interaction (PPI) network analysis screened HF-related genes, including peroxisome proliferator-activated receptor gamma (PPARG), tumor necrosis factor (TNF), and TGF-β1. …”
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