Analysis of gene expression difference and biological process in chorionic villi of unexplained recurrent spontaneous abortion by Linling Shi, Lun Wei, Meiqiu Lu, Hongmei Ding, Le Bo

“…Finally, hub genes were identified through constructing the protein-protein interaction (PPI) network from the differentially expressed gene dataset in the STRING database. …”
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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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Protective effect and mechanism of Sufentanil on acute lung injury in septic mice by Hongqiao Hou, Bowen Jiang, Aiqing Zhu, Junjun Hou, Zhe Qu, Ruping Liu, Aiqun Li

“…To this end, a protein-protein interaction (PPI) network for common targets was first constructed with Swiss Target Prediction Database, GeneCards Database, Draw Venn Diagram Software, STRING 11.5 Database, Cytoscape 3.10.0 Software and Metascape Database, and then key targets were subject to enrichment analysis by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to obtain the key targets of Sufentanil for the treatment of pulmonary sepsis, and then verified by animal experiments. …”
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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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Mechanism of <italic>Hedyotis Diffusa</italic> in Treatment of Osteosarcoma based on Network Pharmacology and Molecular Docking by Qin LIU, Xinwei DUAN, Xihai LI

“…Cytoscape 3.8.1 software was used to construct the compound-target gene network of Hedyotis diffusa; the common target genes were introduced into the STRING database to construct protein-protein interaction(PPI)network; DAVID online database and R language were used to conduct GO enrichment analysis and KEGG enrichment analysis for common targets; Cytoscape 3.8.1 software was used to screen out the core targets of Hedyotis diffusa for intervening osteosarcomas. …”
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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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Joint exploration of network pharmacology and metabolomics on the effects of traditional Chinese medicine compounds in weaned yaks by Sijia Lu, Yanbin Zhu, Yanbin Zhu, Xiaojuan Zhang, Yangji Cidan, Wangdui Basang, Kun Li

“…We explored the possible molecular mechanisms of these TCM formulas using network pharmacology analysis and investigated their effects on the physiology of yaks through metabolomics.ResultsNetwork pharmacology analysis revealed several key target proteins in the protein–protein interaction (PPI) network between three formulas and immune-related genes, including PIK3R1, PIK3CA, JAK2, PTK2, and PYPN11. …”
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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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A Proteomic Study Based on Home Quarantine Model Identifies NQO1 and Inflammation Pathways Involved in Adenoid Hypertrophy by Chen P, Hou S, Pang X, Li L, Wei W

“…Differences in protein expression were analyzed using Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis, Protein-protein interaction, and immunohistochemistry analysis.Results: Long-term home quarantine had a profound impact on the proteomics of pediatric adenoids, with up-regulated and down-regulated proteins of 28 and 92 downregulated proteins, respectively. …”
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The Human Milk-derived Peptide Drives Rapid Regulation of Macrophage Inflammation Responses in the Neonatal IntestineSummary by Fuqiang Yuan, Xu Han, Masha Huang, Yinglin Su, Yiting Zhang, Mengyuan Hu, Xiang Yu, Weilai Jin, Yun Li, Le Zhang

“…Immunofluorescence analysis was used to determine its distribution, and its impact on NF-κB signaling and inflammation was studied in bone marrow-derived macrophages (BMDMs) and intestinal macrophages. Protein-protein interaction (PPI) analysis, single-cell RNA-seq (scRNA-seq), and co-immunoprecipitation (co-IP) experiments were conducted to explore the mechanism underlying CASB135-150 function. …”
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Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis by Abu Tayab Moin, Md. Asad Ullah, Jannatul Ferdous Nipa, Mohammad Sheikh Farider Rahman, Afsana Emran, Md. Minhazul Islam, Swapnil Das, Tawsif Al Arian, Mohammad Mahfuz Enam Elahi, Mukta Akter, Umme Sadea Rahman, Arnab Halder, Shoaib Saikat, Mohammad Jakir Hosen

“…Differentially expressed genes (DEGs) were identified, and their functional roles were assessed through pathway enrichment and tissue-specific expression analysis. Protein-protein interaction (PPI) networks and co-expression modules were constructed to identify hub genes and their associations with disease severity. …”
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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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Exploring the shared gene signatures and mechanism among three autoimmune diseases by bulk RNA sequencing integrated with single-cell RNA sequencing analysis by Xiaofang Liu, Bin Li, Yuxi Lin, Xueying Ma, Yingying Liu, Lili Ma, Xiaomeng Ma, Xia Wang, Nanjing Li, Xiaoyun Liu, Xiaohong Chen

“…Functional enrichment analyses and Protein-Protein Interaction (PPI) network was constructed. We used machine learning algorithms to select candidate biomarkers and evaluate their diagnostic value. …”
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Disrupted mitochondrial morphology and function exacerbate inflammation in elderly-onset ulcerative colitis by Mengmeng Zhang, Hong Lv, Xiaoyin Bai, Gechong Ruan, Qing Li, Kai Lin, Hong Yang, Jiaming Qian

“…ALDH1L1 was identified as a hub DEG through protein–protein interaction networks of RNA-seq, which was downregulated in UC patients or colitis mice versus healthy controls. …”
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Identification of RAD51AP1 as a key gene in hepatitis B virus-associated hepatocellular carcinoma by Meiling Wan, Yonghong Wang, Xiaoling Liu, Yaling Li, Cunliang Deng, Changfeng Sun

“…Methods: HBV-associated HCC datasets (GSE19665, GSE121248, GSE55092, GSE94660, and TCGA-LIHC) acquired from public databases were mined to identify key driver genes by differentially expressed gene analysis, weighted gene co-expression network analysis (WGCNA), followed by protein-protein interaction network analysis, Lasso-Cox regression analysis, and randomforestSRC algorithm. …”
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Six-Gene Signature Associated with Immune Cells in the Progression of Atherosclerosis Discovered by Comprehensive Bioinformatics Analyses by Bin Zhao, Dan Wang, Yanling Liu, Xiaohong Zhang, Zheng Wan, Jinling Wang, Ting Su, Linshan Duan, Yan Wang, Yuehua Zhang, Yilin Zhao

“…Methods. 29 samples of atherosclerosis-related gene expression profiling, including 16 human advanced atherosclerosis plaque (AA) and 13 human early atherosclerosis plaque (EA) samples from the Gene Expression Omnibus (GEO) database, were analyzed to get differentially expressed genes (DEGs) and the construction of protein and protein interaction (PPI) networks. Besides, we detected the relative fraction of 22 immune cell types in atherosclerosis by using the deconvolution algorithm of “cell type identification by estimating relative subsets of RNA transcripts (CIBERSORT).” …”
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Exploring the Anti-PANoptosis Mechanism of Dachaihu Decoction Against Sepsis-Induced Acute Lung Injury: Network Pharmacology, Bioinformatics, and Experimental Validation by Yang Z, Kao X, Zhang L, Huang N, Chen J, He M

“…Nevertheless, The mechanisms of DCHD against SALI via anti-PANoptosis remains unknown.Methods: First, we identified the intersecting targets among DCHD, SALI, and PANoptosis using relevant databases and published literature. Then, protein-protein interaction (PPI) network, molecular docking, and functional enrichment analysis were conducted. …”
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