Identification and Validation of the Pyroptosis-Related Hub Gene Signature and the Associated Regulation Axis in Diabetic Keratopathy by Yi Cui, Li Wang, Wentao Liang, Li Huang, Shuting Zhuang, Hong Shi, Nuo Xu, Jianzhang Hu

“…An integrated bioinformatics pipeline, including differentially expressed gene (DEG) identification, enrichment analysis, protein-protein interaction (PPI) network, coexpression, drug prediction, and immune deconvolution analyses, identified hub genes and key drivers in DK pathogenesis. …”
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Analysis of differentially expressed genes in hypertension and hypertensive cerebral hemorrhage via RNA-sequencing by Hongwu Qi, Min Qiao, Yansong Liu, Weijun Zeng, Lizhao Zhang, Hongjun Guo

“…Functional annotation and protein–protein interaction (PPI) network construction of HT- and HCH-specific DEGs were conducted. …”
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Identification of biomarkers associated with coronary artery disease and non-alcoholic fatty liver disease by bioinformatics analysis and machine learning by Chuan Lu, Mei Han, Qiqi Ma, Li Ying, Yue Zhang

“…We downloaded CAD and NAFLD datasets from the Gene Expression Omnibus (GEO) database and analyzed the differentially expressed genes (DEGs) by limma. Protein–protein interaction (PPI) network was constructed with common DEGs (co-DEGs), and hub genes were screened by Maximal Clique Centrality (MCC) algorithm. …”
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Identification and validation of key autophagy-related genes in lupus nephritis by bioinformatics and machine learning. by Su Zhang, Weitao Hu, Yelin Tang, Xiaoqing Chen

“…Differentially expressed autophagy-related genes (DE-ARGs) among DEGs, key module genes and autophagy-related genes (ARGs) were obtained by venn plot, and subjected to protein-protein interaction network construction. Two machine learning methods were applied to identify signature genes. …”
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The functional insight into the genetics of cardiovascular disease: results from the post-GWAS study by L. O. Bryzgalov, E. E. Korbolina, I. S. Damarov, T. I. Merkulova

“…Functional pathway enrichment and protein– protein interaction (PPI) network analyses were performed on the targets and the extended genes by STRING and DAVID. …”
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MicroRNA-Based Markers of Oral Tongue Squamous Cell Carcinoma and Buccal Squamous Cell Carcinoma: A Systems Biology Approach by Setareh Shojaei, Pouya Menbari, Shokoofeh Jamshidi, Amir Taherkhani

“…With the use of the STRING database, a protein interaction map (PIM) was created. Using the Cytoscape program, hub genes and clusters within the PIM were shown. …”
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Active Ingredients and Potential Mechanism of Additive Sishen Decoction in Treating Rheumatoid Arthritis with Network Pharmacology and Molecular Dynamics Simulation and Experimenta... by Ren J, Liu Z, Qi X, Meng X, Guo L, Yu Y, Dong T, Li Q

“…Additive Sishen decoction (ASSD) is a widely used traditional Chinese medicine for the treatment of RA; however, its active ingredients and the mechanism of its therapeutic effects remain unclear.Methods: To predict the ingredients and key targets of ASSD, we constructed “drug-ingredient-target-disease” and protein–protein interaction networks. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the potential mechanism. …”
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Differential detoxification enzyme profiles in C-corn strain and R-rice strain of Spodoptera frugiperda by comparative genomic analysis: insights into host adaptation by Ping-Hong Yao, Syed Husne Mobarak, Mao-Fa Yang, Chao-Xing Hu

“…Functional predictions and protein interaction networks suggest a broader expansion of metabolism-related genes in the R strain compared to the C strain. …”
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The multi-target mechanism of action of Selaginella doederleinii Hieron in the treatment of nasopharyngeal carcinoma: a network pharmacology and multi-omics analysis by Huaguo Liang, Caifu Fang, Meng Qiu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these genes are primarily involved in critical biological processes like protein phosphorylation and cell cycle regulation. A protein–protein interaction network was constructed, and cytoHubba identified six key genes (BCL2, MAPK14, ABCB1, PLK1, ATM, HMOX1). …”
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Investigation of Scutellaria Barbata’s immunological mechanism against thyroid cancer using network pharmacology and experimental validation by Gen Ouyang, Yuangui Zhu, Zhehao Ouyang

“…TC targets were then filtered, and common targets were selected to build a protein-protein interaction network. GO and KEGG enrichment analyses were performed. …”
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Identification of important genes related to ferroptosis in early missed abortion based on WGCNA by Yulu Zeng, Jiayi Gan, Jinlian Cheng, Changqiang Wei, Xiangyun Zhu, Shisi Wei, Lihong Pang

“…An analysis of the protein-protein interaction (PPI) network was conducted on DEFRGs, identifying five central genes (TP53, EZH2, TIMP1, SLC3A2, and GABARAPL2) using STRING and Cytohubba ROC curves. …”
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Mechanistic insights into epithelial-mesenchymal transition mediated cisplatin resistance in ovarian cancer by Taha Umair Wani, Hyun-Yi Kim, Geum-Hwa Lee, Young Je Lim, Han-Jung Chae, Ji-Ye Kim, Hyonok Yoon

“…This was further confirmed by the protein-protein interaction (PPI) analysis where we identified that the core ECM components e.g., collagen, fibronectin, metalloproteases and integrins possessed most interactions. …”
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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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Expression divergence of BAG gene family in maize under heat stress by Babar Farid, Muhammad Abu Bakar Saddique, Muhammad Hammad Nadeem Tahir, Rao Muhammad Ikram, Zulfiqar Ali, Waseem Akbar

“…Furthermore, the protein-protein interaction networks of ZmBAG-8 and ZmBAG-11 further elucidated their role in stress tolerance related pathways. …”
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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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