An Investigation of the Anticancer Mechanism of <i>Caesalpinia sappan</i> L. Extract Against Colorectal Cancer by Integrating a Network Pharmacological Analysis and Experimental Va... by Mibae Jeong, Jaemoo Chun, Sang-Min Park, Heerim Yeo, Se Won Na, In Jin Ha, Bonglee Kim, Mi-Kyung Jeong

“…The network pharmacological approach identified 87 overlapping genes between CSE targets and CRC-related genes, with protein–protein interaction analysis highlighting 33 key target genes. …”
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Identification and Expression Analysis of Sugar Transporter Gene Family in Aspergillus oryzae by Gongbo Lv, Chunmiao Jiang, Tiantian Liang, Yayi Tu, Xiaojie Cheng, Bin Zeng, Bin He

“…Furthermore, expression profiles of AoSUT genes under salt stress showed that AoSUT genes may be closely linked to salt tolerance and involved in sophisticated transcriptional process. The protein-protein interaction network of AoSUT propounded some potentially interacting proteins. …”
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Alzheimer’s disease may develop from changes in the immune system, cell cycle, and protein processing following alterations in ribosome function by Akiko Yamakawa, Mutsumi Suganuma, Risa Mitsumori, Shumpei Niida, Kouichi Ozaki, Daichi Shigemizu

“…Pathway analyses using these DEGs, followed by protein–protein interaction network analysis, revealed key roles of ribosomal function in MCI progression, whereas immune responses, cell cycle, and protein processing in endoplasmic reticulum were involved in AD progression. …”
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Identification of the Key Genes and Pathways in Esophageal Carcinoma by Peng Su, Shiwang Wen, Yuefeng Zhang, Yong Li, Yanzhao Xu, Yonggang Zhu, Huilai Lv, Fan Zhang, Mingbo Wang, Ziqiang Tian

“…Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction were performed to obtain the biological roles of DEGs in EC. …”
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Proteomic analysis reveals the difference between the spermatozoa of young and old Sus scrofa by Shuhao Fan, Fan Xie, Qianqian Wang, Haibo Ye, Yali Tian, Yangguang Liu, Huibin Zhang, Xianrui Zheng, Zongjun Yin, Xiaodong Zhang

“…KEGG enrichment analysis demonstrated that the differential proteins predominantly resided within the ribosome pathway. A protein-protein interaction (PPI) network was constructed to identify core proteins such as Small ribosomal subunit protein uS7 (RPS5). …”
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A multilayered regulatory network mediated by protein phosphatase 4 controls carbon catabolite repression and de-repression in Magnaporthe oryzae by Zhicheng Huang, Qing Wang, Yan Li, Pengyun Huang, Jian Liao, Jing Wang, Hui Li, Yingying Cai, Jiaoyu Wang, Xiaohong Liu, Fu-Cheng Lin, Jianping Lu

“…We demonstrate that the protein phosphatase 4 complex (Pp4c and Smek1 subunits), the AMP-activated protein kinase (AMPK) Snf1, and the transcriptional regulators CreA (repressor) and Crf1 (activator) collaboratively regulate the utilization of non-preferred carbon sources. Protein interaction and phosphorylation analyses reveal that under glucose-rich conditions, Snf1 and Smek1 directly regulate the phosphorylation status of CreA and Crf1. …”
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Network pharmacology-based screening of the active ingredients and mechanisms of Cymbaria daurica against diabetes mellitus by Ruyu Shi, Dongxue Chen, Mingyue Ji, Baochang Zhou, Ziyan Zhang, Chunhong Zhang, Minhui Li

“…Based on data mining techniques involving topological parameters, gene ontology, and pathway enrichment, we established a compound-target, protein-protein interaction, and target-pathway network to identify central targets and pathways. …”
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STAT1, IGF1, RAC1, and MDM2 Are Associated with Recurrence of Giant Cell Tumor of Bone by Shuxin Chen, Zepeng Du, Bingli Wu, Huiyang Shen, Chunpeng Liu, Xueli Qiu, Yufeng Zhang, Liyan Xu, Enmin Li, Zhigang Zhong

“…The correlation between the expression of these four genes and clinical characteristics was evaluated. Protein-protein interaction (PPI) network was constructed for functional enrichment analysis. …”
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Identifying preeclampsia-associated key module and hub genes via weighted gene co-expression network analysis by Jie Li, Lingling Jiang, Haili Kai, Yang Zhou, Jiachen Cao, Weichun Tang

“…Next, the search tool for the retrieval of interacting genes database (STRING) was adopted to structure the protein-protein interaction (PPI) of genes in the hub module. Furthermore, the MCODE plug-in was applied to discern hub clusters of the PPI network. …”
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Combination of triciribine and p38 MAPK inhibitor PD169316 enhances the differentiation effect on myeloid leukemia cells. by Yuri Sato-Nagaoka, Susumu Suzuki, Souma Suzuki, Shinichiro Takahashi

“…Pathway analysis using DAVID software indicated that "viral protein interaction with cytokine and cytokine receptor" and "cytokine-cytokine receptor interaction" were enriched with high significance. …”
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Identification of Key Genes and Pathways Involved in Circulating Tumor Cells in Colorectal Cancer by Ruijun Pan, Chaoran Yu, Yanfei Shao, Hiju Hong, Jing Sun, Zhou Zhang, Peiyong Li, Minhua Zheng

“…For identification of key genes and pathways, GSE31023, contained CTCs from six metastatic CRC patients and three controls, was retrieved for differentially expressed gene (DEG) analysis. Protein-protein interaction networks of DEGs were constructed. Hub genes from the network were prognostic analyzed, as well as the association with tumor-infiltrating immune cells. …”
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Recombinant SpTransformer proteins bind to specific sites on sea urchin phagocytes and modulate SpTransformer gene expression and immune responsiveness by Ryley S. Crow, Leon Grayfer, L. Courtney Smith

“…A recombinant (r)SpTrf protein interacts specifically with a variety of non-self targets. …”
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Network Pharmacology and Molecular Docking Analyses of the Synergistic Mechanism of Babao Dan and Oxaliplatin in Colorectal Cancer by TAN Jingzhuang, HE Yanbin, HUANG Bin, LIN Jiumao

“…After the intersection and mapping of drugs and disease, the protein-protein interaction (PPI) network and core targets were obtained using STRING database and CytoScape software. …”
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Identification and Validation of a Potential Stemness-Associated Biomarker in Hepatocellular Carcinoma by Yangyang Zhang, Ruike Zhang, Lingxiu Zeng, Haizhou Wang, Ruyi Peng, Meng Zhang, Hailin Zhang, Zhenwei Yang, Liping Gao, Meng Wang, Jing Liu

“…Weighted gene coexpression network analysis (WGCNA) and the protein-protein interaction (PPI) network were performed, and the genes were screened through the Cytoscape software. …”
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Exploration of the Potential Mechanisms of Wumei Pill for the Treatment of Ulcerative Colitis by Network Pharmacology by Jinke Huang, Yijun Zheng, Jinxin Ma, Jing Ma, Mengxiong Lu, Xiangxue Ma, Fengyun Wang, Xudong Tang

“…Based on the identified overlapping common targets, drug-ingredient-target gene network, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) analysis were conducted. Molecular docking was carried out to verify the selected key active ingredients and core targets. …”
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Identification of Differentially Expressed Genes in COVID-19 and Integrated Bioinformatics Analysis of Signaling Pathways by Linjie Fang, Tingyu Tang, Mengqi Hu

“…Finally, with the help of STRING tools, the PPI (protein-protein interaction) network diagrams of DEGs were constructed. …”
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CTSK and PLAU as Prognostic Biomarker and Related to Immune Infiltration in Pancreatic Cancer: Evidence from Bioinformatics Analysis and qPCR by Yuntao Ding, Zhangzuo Li, Huizhi Wang, Qi Wang, Han Jiang, Zhengyue Yu, Min Xu

“…This study utilized microarray datasets (GSE15471, GSE62165, and GSE28735) from the Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs) and construct a protein-protein interaction network using STRING and Cytoscape. …”
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The molecular view of mechanical stress of brain cells, local translation, and neurodegenerative diseases by T. M. Khlebodarova

“…The roles of the mTOR (mammalian target of rapamycin) signaling pathway; the RNA-binding FMRP protein; the CYFIP1 protein, interacting with FMRP; the family of small GTPases; and the WAVE regulatory complex in the regulation of translation initiation and actin cytoskeleton rearrangements in dendritic spines of the activated synapse are discussed. …”
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Potential Biomarkers and Signaling Pathways Associated with the Pathogenesis of Primary Ameloblastoma: A Systems Biology Approach by Zeynab Bayat, Azin Mirzaeian, Amir Taherkhani

“…The dataset GSE132472 was obtained from the GEO database, and multivariate statistical analyses were applied to identify differentially expressed genes (DEGs) in primary ameloblastoma tissues compared to the corresponding normal gingiva samples. A protein-protein interaction (PPI) map was built using the STRING database. …”
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Integrating network pharmacology and experimental validation to explore the pharmacological mechanism of Astragaloside IV in alleviating urotensin II-mediated renal tubular epithel... by Wenyuan Liu, Qianwei Liu, Ziyuan Zhang, Yaling Hu, Jingai Fang

“…DAVID software was then used to perform GO and KEGG enrichment analysis on these target genes, and STRING and cytoscape were used to construct a protein interaction network. Molecular docking analysis was performed on key genes. …”
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