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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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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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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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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Bioinformatics Analysis of Exercise-Related Biomarkers in Diabetes by Xiaoju Bao, Jingyue Qiu, Qin Xuan, Xinming Ye

“…Next, the protein-protein interaction (PPI) network maps were drawn, and the hub genes were identified through Metascape. …”
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5-Aminolevulinic acid activates the MdWRKY71-MdMADS1 module to enhance anthocyanin biosynthesis in apple by Liuzi Zhang, Huihui Tao, Jianting Zhang, Yuyan An, Liangju Wang

“…Additionally, we discovered that MdWRKY71 independently binds to and activates the transcription of two other anthocyanin biosynthetic genes, MdANS and MdDFR. The protein–protein interaction between MdWRKY71 and MdMADS1 amplifies the transcriptional activation of these genes by MdWRKY71. …”
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The Immune Landscape of Hepatitis B Virus-Related Acute Liver Failure by Integration Analysis by Jiao Gong, Yaqiong Chen, Jing Cao, Yang Wang, Jiahao Chen, Danyang Li, Liuping Sha, Xinhua Li, Yutian Chong, Bo Hu

“…The enrichment scores of cell death gene sets from Kyoto Encyclopedia of Genes and Genomes (KEGG) were calculated by gene set variation analysis method, and a protein-protein interaction (PPI) network was constructed using Cytoscape. …”
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Combination of Enrichment Using Gene Ontology and Transcriptomic Analysis Revealed Contribution of Interferon Signaling to Severity of COVID-19 by Hilmi Farhan Ramadhani, Annisa Annisa, Aryo Tedjo, Dimas R. Noor, Wisnu Ananta Kusuma

“…One of the appropriate methods to functionally group large-scale protein-protein interaction (PPI) data into small-scale clusters is fuzzy K-partite clustering. …”
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Using Network Pharmacology and Animal Experiment to Investigate the Therapeutic Mechanisms of Polydatin against Vincristine-Induced Neuropathic Pain by Peng Xi, Rui Mao, Shiyan Wu, Lei Liu, Ceng Cai, Lei Lu, Cailin Zhang, Yimei Li

“…Subsequently, the intersection targets were obtained using the Venn tool, and the protein-protein interaction (PPI) was constructed by the STRING database. …”
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New insights into the mechanism of triphenyl phosphate and its metabolite diphenyl phosphate in diabetic kidney disease by Ting Fang, Qiaoyan Liu, Xinxin Huangfu, Hongkai Zhu, Hongwen Sun, Liming Chen

“…Additionally, the study explored the targets of action for TPHP and DPHP using network toxicity analysis, conducted protein interaction analysis, and explored the functional aspects of action through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. …”
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Conserved Nuclear Localization Signal in NS2 Protein of Bombyx Mori Bidensovirus: A Potential Invertebrate ssDNA Virus Trait by Qian Yu, Jiaxin Yan, Ying Chen, Jinfeng Zhang, Qi Tang, Feifei Zhu, Lindan Sun, Shangshang Ma, Xiaoyong Liu, Keping Chen, Qin Yao

“…Additionally, co-immunoprecipitation and mass spectrometry were utilized to identify host proteins interacting with NS2. We identified a functional bipartite NLS in NS2, validated the combination pattern of key amino acids, and demonstrated its role in regulating viral promoter activity. …”
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