Macrophages Phenotype Regulated by IL-6 Are Associated with the Prognosis of Platinum-Resistant Serous Ovarian Cancer: Integrated Analysis of Clinical Trial and Omics by Xiaoqing Wu, Wenping Lu, Chaojie Xu, Cuihong Jiang, Zhili Zhuo, Ruipeng Wang, Dongni Zhang, Yongjia Cui, Lei Chang, Xi Zuo, Ya’nan Wang, Heting Mei, Weixuan Zhang, Mengfan Zhang, Chen Li

“…The differential expression genes (DEGs) were analyzed via protein–protein interaction network, Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis to reveal major pathways of DEGs. …”
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Exploring the Causal Relationship and Molecular Mechanisms Between Fasting Insulin and Androgenetic Alopecia: A Mendelian Randomization Study with Bioinformatics Analysis by Ding X, Bai Z, Wang W, Gu Y, Li Z, Fan Y

“…FI-associated genes were identified through expression quantitative trait loci (eQTL) analysis, with enrichment analysis and a protein-protein interaction (PPI) network used to explore potential pathways and core genes.Results: Forward MR analysis revealed a significant causal relationship between elevated FI levels and AGA (P=0.027, OR=43.944). …”
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Mechanistic insights into pachymic acid’s action on triple-negative breast Cancer through TOP2A targeting by Ming Liu, Li Zheng, Yang Zhang, Jinhui Tian

“…The STRING interaction network analysis tool was used to create Protein-Protein Interaction (PPI) networks. Enrichment analysis included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). …”
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Integrative physiological and transcriptome analysis unravels the mechanism of low nitrogen use efficiency in burley tobacco by Yuqing Feng, Yuanyuan Zhao, Yanjun Ma, Xiaolong Chen, Hongzhi Shi

“…In addition, the protein–protein interaction (PPI) network diagram identified eight key genes (TPIP1, GAPB, HEMB, PGK3, PSBO, PSBP2, PSAG, and GLN2) that may affect NUE. …”
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Upregulated GSDMB in Clear Cell Renal Cell Carcinoma Is Associated with Immune Infiltrates and Poor Prognosis by Yuanshan Cui, Zhongbao Zhou, Yumeng Chai, Yong Zhang

“…Relationships between GSDMB expression, clinicopathological variables, and overall survival (OS) were evaluated with multivariate methods as well as Kaplan-Meier survival curves. Protein-protein interaction (PPI) networks were created with STRING. …”
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Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning by Wei Chen, Zeyan Xu, Haitao Sun, Wen Feng, Zhenhua Huang

“…Key genes were selected by combining hub genes from the protein-protein interaction (PPI) network with feature genes identified by Lasso and Random Forest (RF) algorithms. …”
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Key wound healing genes as diagnostic biomarkers and therapeutic targets in uterine corpus endometrial carcinoma: an integrated in silico and in vitro study by Fuchuan Jiang, Sajjad Ahmad, Sadia kanwal, Yasir Hameed, Qian Tang

“…Results Seventy wound healing-associated genes were extracted from the Gene Ontology (GO) database, and a protein-protein interaction (PPI) network was constructed using the STRING database. …”
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Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle by Yan Peng, Xianwen Zhang, Yuewu Liu, Xinbo Chen

“…Finally, a heat-induced miRNA-PPI (protein-protein interaction) network was constructed, and three miRNA coregulatory modules were discovered.…”
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Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling by Chaofan Shan, Kui Dong, Dongyu Wen, Ziyi Ye, Fei Hu, Meryem Zekraoui, Jun Cao

“…Furthermore, the protein interaction network revealed their interactions with a number of proteins of significant functional importance. …”
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Identification of Key Genes and Prognostic Value Analysis in Hepatocellular Carcinoma by Integrated Bioinformatics Analysis by Meng Wang, Licheng Wang, Shusheng Wu, Dongsheng Zhou, Xianming Wang

“…The functional and pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of the identified DEGs was constructed using the Search Tool for the Retrieval of Interacting Gene, and hub genes were identified. …”
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Orientin Reduces the Effects of Repeated Procedural Neonatal Pain in Adulthood: Network Pharmacology Analysis, Molecular Docking Analysis, and Experimental Validation by Dong-Dong Guo, Hai-Yan Huang, Hai-E. Liu, Kun Liu, Xing-Jing Luo

“…Several compound-protein databases and disease-protein databases were employed to identify proteins that were both predicted targets of orientin and involved in neonatal pain. A protein-protein interaction (PPI) network was constructed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential mechanism of action. …”
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Network pharmacology and molecular analysis of mechanisms underlying the therapeutic effects of Rhubarb in treating atherosclerosis and abdominal aortic aneurysm by Huilin Xu, Jun Huang, Youjie Zeng, Xia Wang, Huilin Lian, Siyi Zhang, Ren Guo

“…Gene interactions were utilized to identify common targets of Rhubarb with AS/AAA, and interaction networks were constructed using Cytoscape 3.9.1. Protein-protein interaction (PPI) networks for the core targets were constructed using the STRING database. …”
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Unveiling the role of melatonin‐related gene CSNK1D in osteoclastogenesis and its implications for osteoporosis treatment by Jiewen Zhang, Shaobo Wu, Fangze Xing, Ning Kong, Yiwei Zhao, Xudong Duan, Yiyang Li, Kunzheng Wang, Run Tian, Pei Yang

“…Functional enrichment, correlation and protein–protein interaction analyses were conducted. Experimental validation involved in vitro differentiation assays using RAW264.7 cells and in vivo studies with an ovariectomy‐induced rat model of OP to evaluate the role of CSNK1D in osteoclastogenesis to verify its effect on OP. …”
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Aerobic capacity and muscle proteome: Insights from a mouse model by Abel Plaza‐Florido, Alejandro Santos‐Lozano, Susana López‐Ortiz, Beatriz G. Gálvez, Joaquín Arenas, Miguel A. Martín, Pedro L. Valenzuela, Tomàs Pinós, Alejandro Lucia, Carmen Fiuza‐Luces

“…The quadriceps muscle proteome was studied using liquid chromatography with tandem mass spectrometry, with the Search Tool for the Retrieval of Interacting Genes/Proteins database used to generate protein–protein interaction (PPI) networks and enrichment analyses. …”
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Transcriptome Analysis and Phytohormone Profile Reveal Core Phytohormone Regulating Parthenocarpy in Fingered Citron by Qianbin Chen, Jinjian Xu, Xinjian Zou, Yanjun Zhang, Xiaoxian Zhu, Kewei Zhang, Wenrong Chen, Fanglei Liao, Weidong Guo

“…A total of 66 differentially expressed hormone-related genes were identified, with the auxin pathway emerging as the most prominent in fingered citron. Protein–protein interaction analysis revealed a potential interaction between auxin and abscisic acid (ABA). …”
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Key regions aberrantly connected within cerebello-thalamo-cortical circuit and their genetic mechanism in schizophrenia: an fMRI meta-analysis and transcriptome study by Yarui Wei, Ziyu Wang, Kangkang Xue, Xiaoyu Niu, Longyao Ma, Shaoqiang Han, Baohong Wen, Yong Zhang, Huafu Chen, Jingliang Cheng

“…These genes were specially expressed in the brain tissue, in the neurons of the cerebellum, subcortex and cortex and during nearly all developmental stages, and constructed a protein-protein interaction network supported by 85 hub genes with functional significance. …”
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A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma by Yingkun Xu, Xiunan Li, Yuqing Han, Zilong Wang, Chenglin Han, Ningke Ruan, Jianyi Li, Xiao Yu, Qinghua Xia, Guangzhen Wu

“…Afterward, using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) website, we established the protein-protein interaction (PPI) network of genes related to the PPAR pathway. …”
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Decreased Spp1 Expression in Acute Myocardial Infarction after Ischemia and Reperfusion Injury by Ling Li, Jungang Huang, Zongkai Zhao, Zhuzhi Wen, Kang Li, Tianjiao Ma, Lisui Zhang, Junmeng Zheng, Shi Liang

“…Furthermore, we constructed a protein-protein interaction (PPI) network. In the end, we used quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blotting to measure and compare the expression of Spp1 in patients who accepted percutaneous coronary intervention. …”
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Identification of Potential Biomarkers and Immune Features of Sepsis Using Bioinformatics Analysis by Fang-Chen Gong, Ran Ji, Yu-Ming Wang, Zhi-Tao Yang, Ying Chen, En-Qiang Mao, Er-Zhen Chen

“…Functional enrichment of the DEGs was analyzed with the DAVID database. Protein-protein interaction networks were derived using the STRING database and visualized using Cytoscape software. …”
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Comprehensive Analysis of Differentially Expressed miRNAs and mRNAs Reveals That miR-181a-5p Plays a Key Role in Diabetic Dermal Fibroblasts by Peng Liu, Yi Zhu, Qin Li, Biao Cheng

“…Subsequently, we constructed the gene correlation network of DEGs to identify hub genes by merging the protein-protein interaction network, weighted gene coexpression network, and predicted miRNA-mRNA regulatory network. …”
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