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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Identification of biomarkers associated with ferroptosis in macrophages infected with Mycobacterium abscessus using bioinformatic tools. by Jiahua Qian, Chenghua Lu, Kai Meng, Zhihong Xu, Honghao Xue, Weijie Yang

“…Additionally, a protein-protein interaction network was built, and functional enrichment analyses were conducted for the hub genes. …”
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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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Fast Skyline Community Search in Multi-Valued Networks by Dongxiao Yu, Lifang Zhang, Qi Luo, Xiuzhen Cheng, Jiguo Yu, Zhipeng Cai

“…Community search has been extensively studied in large networks, such as Protein-Protein Interaction (PPI) networks, citation graphs, and collaboration networks. …”
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Expression Profiling of Proliferation and Apoptotic Markers along the Adenoma-Carcinoma Sequence in Familial Adenomatous Polyposis Patients by Jayson Wang, Nabil El-Masry, Ian Talbot, Ian Tomlinson, Malcolm R. Alison, Mona El-Bahrawy

“…Familial adenomatous polyposis (FAP) patients have a germline mutation in the adenomatous polyposis coli (APC) gene. The APC protein interacts with beta-catenin, resulting in the activation of the Wnt signalling pathway. …”
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Integrated Transcriptome Analysis Reveals Novel Molecular Signatures for Schizophrenia Characterization by Tong Ni, Yu Sun, Zefeng Li, Tao Tan, Wei Han, Miao Li, Li Zhu, Jing Xiao, Huiying Wang, Wenpei Zhang, Yitian Ma, Biao Wang, Di Wen, Teng Chen, Justin Tubbs, Xiaofeng Zeng, Jiangwei Yan, Hongsheng Gui, Pak Sham, Fanglin Guan

“…The biological relevance of these DREGs is examined through protein–protein interaction network, pathway enrichment, polygenic scoring, and brain tissue expression. …”
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CENPN contributes to pancreatic carcinoma progression through the MDM2-mediated p53 signaling pathway by Ming Xu, Jie Tang, Qiong Sun, Jing Meng, Guoyu Chen, Yunli Chang, Yao Yao, Jieru Ji, Hao Luo, Lingling Chen, Minxue Lu, Weiwei Shi

“…Material and methods The construction of a protein-protein interaction (PPI) network was based on overlapping differentially expressed genes (DEGs) identified in the GSE16515, GSE32676, and GSE125158 datasets. …”
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The anti-cancerous mechanism of licochalcone A on human hepatoma cell HepG2 based on the miRNA omics by Jun Wang, Xiuxiu Zhang, Zhijing Ni, Elnur Elam, Kiran Thakur, Kexin Li, Chuyan Wang, Jianguo Zhang, Zhaojun Wei

“…FoxO signaling pathway was the hub pathway for the targets. A protein-protein interaction network was structured on the STRING platform to discover the hub genes. …”
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Targeting p62 by sulforaphane promotes autolysosomal degradation of SLC7A11, inducing ferroptosis for osteosarcoma treatment by Qiuming Zou, Xiaofeng Zhou, Jianqin Lai, Haixia Zhou, Jinxuan Su, Zhijing Zhang, Xiaosong Zhuang, Lili Liu, Ruijie Yuan, Sijia Li, Siyu Yang, Xinyi Qu, Jiezhu Feng, Yongqi Liu, Zisheng Li, Shiting Huang, Zhi Shi, Yu Yan, Zhiming Zheng, Wencai Ye, Qi Qi

“…Mechanically, SFN directly targeted p62 protein and enhanced p62/SLC7A11 protein-protein interaction, thereby promoting the lysosomal degradation of SLC7A11 and triggering ferroptosis. …”
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Mechanism of Cordyceps Cicadae in Treating Diabetic Nephropathy Based on Network Pharmacology and Molecular Docking Analysis by Yi Qian, Xin Sun, Xin Wang, Xin Yang, Mengyao Fan, Jiao Zhong, Zejun Pei, Junping Guo

“…The network of active components and targets was drawn by Cytoscape 3.6.0, the protein-protein interaction (PPI) was analyzed by the STRING database, and the DAVID database was used for the enrichment analysis of intersection targets. …”
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The Identification of Key Genes and Pathways in Glioma by Bioinformatics Analysis by Mingfa Liu, Zhennan Xu, Zepeng Du, Bingli Wu, Tao Jin, Ke Xu, Liyan Xu, Enmin Li, Haixiong Xu

“…Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied for the enriched pathways. A protein-protein interaction (PPI) network was constructed to find the hub genes. …”
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Personalized prediction of anticancer potential of non-oncology drugs through learning from genome derived molecular pathways by Xiaobao Dong, Huanhuan Liu, Ting Tong, Liuxing Wu, Jianhua Wang, Tianyi You, Yongjian Wei, Xianfu Yi, Hongxi Yang, Jie Hu, Haitao Wang, Xiaoyan Wang, Mulin Jun Li

“…Utilizing protein–protein interaction networks, CHANCE harmonizes multilevel mutation annotations and integrates pharmacological information across different drugs into a single model. …”
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Proteome differences of dental stem cells between permanent and deciduous teeth by data-independent acquisition proteomics by Zhang Suping, Liu Yuqing, Dong Jin, Jiao Min, Gu Yongchun, Chen Liling, Yuan Na, Wang Jianrong, Yang Dezhao, Meng Fanwen

“…Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, along with protein–protein interaction network construction, revealed significant metabolic differences and key regulatory nodes. …”
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Genome-Wide Identification and Analysis of the Cytochrome B5 Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis) by Han Zheng, Xin Li, Lin Shi, Ying Jing, Qingqing Song, Yanan Chen, Lilong He, Fengde Wang, Jianwei Gao, Yuping Bi

“…Phylogenetic analysis of the CB5 protein sequences from six species showed that the BrCB5s conduct a close evolutionary process with the CB5s of Arabidopsis thaliana and far from those of Oryza sativa. Protein interaction analysis showed that 40 interaction patterns were predicted including two Sucrose Transporter 4 subfamily proteins (SUT 4) and Fatty Acid Hydroxylase 2 protein (FAH 2) can interact with most members of BrCB5s. …”
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Comparative analysis of HKTs in six poplar species and functional characterization of PyHKTs in stress-affected tissues by Xiaojiao Liu, Lincui Shi, Hezi Bai, Jing Wang, Anmin Yu, Aizhong Liu, Ping Li

“…Furthermore, cis-element analysis and protein interaction predictions provide insights into the functions of HKTs under salt stress through the activation of ion transporters, proline content, and ATPases regulated by hormonal signals and MYB transcription factors. …”
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