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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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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Transcriptome, miRNA, and degradome sequencing reveal the leaf stripe (Pyrenophora graminea) resistance genes in Tibetan hulless barley by Yue Wang, Qian Hu, Youhua Yao, Yongmei Cui, Yixiong Bai, Likun An, Xin Li, Baojun Ding, Xiaohua Yao, Kunlun Wu

“…Based on the above research results, we constructed a Protein-Protein Interaction (PPI) network of barley leaf stripe resistance. …”
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Puerarin Ameliorates the Ferroptosis in Diabetic Liver Injure Through the JAK2/STAT3 Pathway Inhibition Based on Network Pharmacology and Experimental Validation by Fan X, Liu S, Yu J, Hua J, Feng Y, Wang Z, Shen Y, Lan W, Wang J

“…However, the mechanism of protective effect of Puerarin on DLI remains unclear.Methods: Various databases were used to screen for targets of Puerarin, ferroptosis and DLI. Protein-protein interaction (PPI) network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to predict key targets and pathways. …”
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Inhibition of complement system-related gene ITGB2 attenuates epithelial–mesenchymal transition and inflammation in diabetic nephropathy by Jun Peng, Wenqi Zhao, Lu Zhou, Kun Ding

“…Weighted Gene Co-expression Network Analysis (WGCNA) was employed to screen the DN-related genes, then the differential CSRGs (DCSRGs) were identified, followed by protein–protein interaction (PPI) network construction. In addition, key biomarkers were acquired by two machine learning algorithms, then immune infiltration analysis, Gene Set Enrichment Analysis (GSEA), and potential drugs screening were conducted. …”
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Compound identification of Shuangxinfang and its potential mechanisms in the treatment of myocardial infarction with depression: insights from LC-MS/MS and bioinformatic prediction by Yize Sun, Yize Sun, Haibin Zhao, Zheyi Wang

“…All the targets were intersected to construct the Protein-Protein Interaction (PPI) network on Metascape platform and the herb-compound-target (HCT) network on Cytoscape, to identify the hub targets. …”
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Identification of Potential miRNA-mRNA Regulatory Network Contributing to Parkinson’s Disease by Xi Yin, Miao Wang, Wei Wang, Tong Chen, Ge Song, Yixuan Niu, Ziying Jiang, Zhongbao Gao, Zhenfu Wang

“…The correlation between the screened genes and PD was evaluated with the online tool Comparative Toxicogenomics Database (CTD), and protein-protein interaction (PPI) networks were built by the STRING platform. …”
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Identification and Analysis of Potential Immune-Related Biomarkers in Endometriosis by Yanan He, Jixin Li, Yanjun Qu, Liyuan Sun, Xibo Zhao, Han Wu, Guangmei Zhang

“…Simultaneously, the Pearson correlation analysis and protein-protein interaction (PPI) analyses were used to indicate the potential mechanisms of TF-IRGs at the molecular level and obtain hub IRGs. …”
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Integrated analysis of cell cycle and p53 signaling pathways related genes in breast, colorectal, lung, and pancreatic cancers: implications for prognosis and drug sensitivity for... by Jiyauddin Khan, Priyanjana Ghosh, Urmi Bajpai, Kountay Dwivedi, Daman Saluja

“…Common cell cycle and p53 signaling genes were acquired from MSigDB using GSEA. A protein–protein interaction network was constructed using STRING and Cytoscape, identifying top hub genes. …”
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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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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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Immune infiltration landscape and potential drug-targeted implications for hepatocellular carcinoma with ‘progression/hyper-progression’ recurrence by Jing-Xuan Xu, Yue-Xiang Su, Yuan-Yuan Chen, Yi-Yue Huang, Zu-Shun Chen, Yu-Chong Peng, Lu-Nan Qi

“…Co-expression and protein interaction analyses were used to identify characteristic genes in ITM closely associated with type III–IV recurrence, which was matched with drug targets for Huaier granules (HG) and lenvatinib. …”
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In silico analysis of hub genes and regulatory networks implicates the putamen in non-motor Parkinson’s disease disorders by Stephen Tunmise Akanbi, Joshua Ayodele Yusuf, Thompson Oluwaferanmi Ayandele, Dayo Samson Oladipupo, Darasimi Racheal Olorunlowu, Blessing Dorcas Olawuyi, Joshua Oluwafisayo Adepoju, Dolapo Emmanuel Opasina, Elizabeth Kehinde Opoola, Uchenna Victor Ugwuanyi, Olufunto Omodele Adeleye

“…Differential gene expression analysis was carried out using with Limma, filtering for genes with |logFC|> 1 (fold change) and p < 0.05 (p-value). Protein–Protein Interaction networks were constructed using stringDB (combined score > 0.7) and analyzed in Cytoscape to identify hub genes based on various topological measures (EPC, MCC, MNC, Degree, and EcCentricity). …”
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Proteomic analysis of spinal dorsal horn in prior exercise protection against neuropathic pain by Binglin Chen, Jiabao Guo, Chan Gong, Chenchen Zhu, Yang Wu, Shengbo Wang, Yili Zheng, Haixia Lu

“…Gene Ontology (GO) annotations, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein–protein interaction networks were employed to explore the biological importance of DEPs. …”
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Bergapten alleviates senescence of chondrocytes in osteoarthritis by YE Yuanlan, LIU Kaiwen, PAN Yiming

“…The obtained targets were intersected with Venny2.1.0, protein-protein interaction (PPI) analysis was performed using the STRING database, and molecular docking was conducted by AutoDock Vina. …”
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Transcriptome analysis of jejunal mucosal tissue in breeder hens exposed to acute heat stress by Yongcai Zhu, Satoshi Kubota, Phocharapon Pasri, Sitthipong Rakngam, Supattra Okrathok, Chayanan Pukkung, Shenglin Yang, Sutisa Khempaka

“…Functional analysis through gene ontology classification, pathway mapping via the Kyoto encyclopedia of genes and genomes, and protein interaction networks identified several important regulatory genes in thermal response (HSPA8 and HSPA2), energy homeostasis and fat metabolism (PDK4, PPARA, and CD36), glucose transport (SLC2A5), and cholesterol synthesis pathway (SQLE, CYP51A1, and HSD17B7). …”
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Cardiovascular Risk Biomarkers in Women with and Without Polycystic Ovary Syndrome by Manjula Nandakumar, Priya Das, Thozhukat Sathyapalan, Alexandra E. Butler, Stephen L. Atkin

“…Functional enrichment and protein–protein interaction analyses elucidated the pathways involved. …”
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CCR7 and CD48 as Predicted Targets in Acute Rejection Related to M1 Macrophage after Pediatric Kidney Transplantation by Jie Zhang, Jun Pei, Chengjun Yu, Jin Luo, Yifan Hong, Yi Hua, Guanghui Wei

“…At the same time, we used the protein–protein interaction (PPI) network and Cytoscape software to determine the key genes. …”
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