Construction of the bromodomain-containing protein-associated prognostic model in triple-negative breast cancer by Wei Chen, Yushuai Yu, Chenxi Wang, Zirong Jiang, Xiewei Huang, Yidan Lin, Hongjing Han, Qing Wang, Hui Zhang

“…Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis were conducted to investigate active pathways and molecular interactions. …”
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Ferroptosis Transcriptional Regulation and Prognostic Impact in Medulloblastoma Subtypes Revealed by RNA-Seq by Christophe Desterke, Yuanji Fu, Jenny Bonifacio-Mundaca, Claudia Monge, Pascal Pineau, Jorge Mata-Garrido, Raquel Francés

“…Using two independent medulloblastoma RNA-sequencing cohorts (MB-PBTA and MTAB-10767), we investigated the expression of ferroptosis-related molecules through multiple approaches, including Weighted Gene Co-Expression Network Analysis (WGCNA), molecular subtype stratification, protein–protein interaction (PPI) networks, and univariable and multivariable overall survival analyses. …”
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MAP17 is a Novel NASH Progression Biomarker Associated with Macrophage Infiltration, Immunotherapy Response, and Oxidative Stress by Huang Z, Chen J, Liu S, Xiang X, Long Y, Tan P, Fu W

“…Our further analyses included differential expression evaluation, protein-protein interaction (PPI) network analysis, and Venn diagram analysis to discover novel targets. …”
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Contribution of cuproptosis and immune-related genes to idiopathic pulmonary fibrosis disease by Chengji Jin, Jia Li, Qiaoyu Li, Lipeng Zhang, Shaomao Zheng, Qiong Feng, Yongjie Li, Yu Zheng, Qiuli Nie, Jin Liang, Jing Wang, Jing Wang

“…Additionally, four immune-related hub genes were screened using a protein–protein interaction (PPI) network and evaluated through the receiver operating characteristic (ROC) curve. …”
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Ferroptosis-related genes participate in the microglia-induced neuroinflammation of spinal cord injury via NF-κB signaling: evidence from integrated single-cell and spatial transcr... by Siqiao Wang, Li Yang, Zhourui Wu, Chen Li, Shaoke Wang, Zhihui Xiao, Bei Ma, Rongrong Zhu, Liming Cheng

“…Through weighted gene co-expression network analysis and differential expression analysis in GSE45006, we identified differentially expressed time- and immune-related genes (DETIRGs) associated with chronic SCI and differentially expressed ferroptosis- and immune-related genes (DEFIRGs), which were validated in GSE151371. Protein–protein interaction and microRNA-mRNA-transcription factor regulatory networks were constructed based on Search Tool for the Retrieval of Interacting Genes (STRING) and NetworkAnalyst, respectively, which were validated by chromatin immunoprecipitation followed by sequencing (ChIP-seq). …”
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Proteomic analysis to explore potential mechanism underlying pseudomale sperm defect in Cynoglossus semilaevis by Xihong Li, Lu Li, Zhongkai Cui, Ming Li, Xuexue Sun, Zhijie Li, Zhangfan Chen, Lanqing Ding, Dongdong Xu, Wenteng Xu

“…Proteins involved with proteasome were enriched by GO and KEGG analyses. A protein-protein interaction (PPI) network was further constructed to understand the relationship of the DEPs. …”
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Genome-Wide Characterization and Expression Analysis of the HD-ZIP Gene Family in Response to Salt Stress in Pepper by Zhongrong Zhang, Ranran Zhu, Xuehua Ji, Hui Ji Li, Hui Lv, Hai Ying Zhang

“…There were multiple pressure-related action elements upstream of the start codon of the HD-Z-IP family. Protein interaction network proved to be coexpression phenomenon between ATML1 (CaH-DZ22, CaHDZ32) and At4g048909 (CaHDZ12, CaHDZ31), and three regions of them were highly homology. …”
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Identification of Three Significant Genes Associated with Immune Cells Infiltration in Dysfunctional Adipose Tissue-Induced Insulin-Resistance of Obese Patients via Comprehensive B... by Ming Zhai, Peipei Luan, Yefei Shi, Bo Li, Jianhua Kang, Fan Hu, Mingjie Li, Lei Du, Donglei Zhou, Weixia Jian, Wenhui Peng

“…DEGs mainly participated in the process of multiple immune cells’ infiltration. In protein-protein interaction network, we identified CSF1R, C1QC, and TYROBP as hub genes. …”
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Identification of EARS2 as a Potential Biomarker with Diagnostic, Prognostic, and Therapeutic Implications in Colorectal Cancer by Wang L, Deng X, Tang J, Gong Y, Bu S, Li Z, Liao B, Ding Y, Dai T, Liao Y, Li Y

“…To investigate the mechanisms underlying EARS2 in CRC, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis, and Protein-Protein Interaction analyses were performed, alongside the construction of miRNA-mRNA interaction networks. …”
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The Multifaceted Roles of Myrrha in the Treatment of Breast Cancer: Potential Therapeutic Targets and Promises by Anwar Shams MD, MSc, PhD, Abdullah Ahmed Alzahrani, Taghreed A Ayash MSc, PhD, Shadi Tamur MD, FRCPC, FAAP, Majed AL-Mourgi MD, FRCS, FCCP, FACS

“…Furthermore, the STRING protein interaction network and the KEGG analyses indicate that myrrh exerts therapeutic effects on breast cancer by regulating several biological processes such as cell proliferation, cell migration, apoptosis, and various signaling pathways, including TNF, PI3K-Akt, NF-κB, and MAPK. …”
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Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.) by Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md. Abdur Rauf Sarkar

“…In addition, 46 putative miRNAs were predicted to target 81 HvlecRLK genes and HvlecRLK13 was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 Arabidopsis STRING proteins. …”
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Potential drug targets for asthma identified through mendelian randomization analysis by Xingxuan Chen, Yu Shang, Danting Shen, Si Shi, Zhe Wen, Lijuan Li, Hong Chen

“…Bidirectional Mendelian randomization analysis, Steiger filtering, colocalization, and phenotype scanning were employed for reverse causal inference detection, further substantiating the Mendelian randomization results. A protein-protein interaction network was also constructed to reveal potential associations between proteins and asthma medications. …”
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Transcriptomic Analysis of Menstrual Blood-Derived Stem Cells Transplantation Combined with Exercise Training in Promoting Spinal Cord Injury Recovery in Rats by QI Longju, CHEN Shiyuan, LIAO Zehua, SHI Yuanhu, SUN Yuyu, WANG Qinghua

“…Differential gene expression, GO (Gene Ontology) functional enrichment, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, and protein-protein interaction (PPI) network analyses were performed. …”
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Identification of the Granule-Bound Starch Synthase (GBSS) Genes Involved in Amylose Biosynthesis in Tartary Buckwheat (<i>Fagopyrum tataricum</i> (L.) Gaertn.) by Juan Huang, Fei Liu, Jieqiong Zhang, Bin Tang, Jiao Deng, Taoxiong Shi, Liwei Zhu, Hongyou Li, Qingfu Chen

“…Furthermore, the cis acting elements in the promoters of <i>FtGBSSs</i> and their binding transcription factors (TFs) were investigated. A protein–protein interaction network was constructed and co-expression was analyzed based on the gene expression patterns of the <i>FtGBSSs</i>, and the identified TFs, belonging to bZIP, ERF, bHLH, and MADS-box TF families, were identified within this network, and their expression patterns were significantly correlated to the expression patterns of two seed-specific <i>FtGBSS</i> genes (<i>FtGBSS-3</i> and <i>FtGBSS-5</i>). …”
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The role of FTO in m6A RNA methylation and immune regulation in Staphylococcus aureus infection-related osteomyelitis by Sijing Liu, Sijing Liu, Sijing Liu, Kai Li, Changhai Long, Mingwu Lao, Biao Ma, Changquan Liu, Haoyuan He, Chunjiang Wang, Wangzhu Chen, Bin Yu

“…Initially, we constructed a diagnostic model based on m6A genes and predicted the hub node miRNAs and transcription factors by constructing a protein–protein interaction network. Subsequently, a prognostic model was built using LASSO regression, the receiver operating characteristic curve of the model was plotted, and the predictive performance of the diagnostic model was validated. …”
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Integrated bioinformatics analysis to explore potential therapeutic targets and drugs for small cell carcinoma of the esophagus by Maofei Zhu, Maofei Zhu, Yueming Chu, Yueming Chu, Qiang Yuan, Qiang Yuan, Junfeng Li, Silin Chen, Lin Li, Lin Li, Lin Li

“…The STRING database was employed to conduct protein-protein interaction (PPI) analysis of differentially expressed onco/tumor suppressor genes, the network was further constructed in Cytoscape, and hub genes of the network were obtained through the Cytohubba plugin. …”
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RETRACTED: Mechanism of action of Asparagus officinalis extract against multiple myeloma using bioinformatics tools, in silico and in vitro study by Yanju Li, Xu Yang, Feiqing Wang, Feiqing Wang, Jianing Zhao, Chike Zhang, Dan Wu, Bo Yang, Rui Gao, Peng Zhao, Yun Zan, Min Su, Zhixu He, Yang Liu, Yang Liu, Yang Liu, Jishi Wang, Dongxin Tang

“…The STRING database and Cytoscape were utilized to create protein–protein interaction (PPI) networks and further screening of core targets.Results: The intersection of target genes and core target genes of the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) pathway was enriched, the top-five core target genes were selected, and the binding affinity of corresponding compounds to the top-five core targets was analyzed using molecular docking. …”
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An integrative analysis reveals cancer risk associated with artificial sweeteners by Jumin Xie, Ying Zhu, Zixuan Yang, Zhang Yu, Mingzhi Yang, Qingzhi Wang

“…A network visualization (‘AS-targets-cancer’) was constructed using Cytoscape 3.9.0. Protein–protein interaction analysis was conducted using the STRING database to identify significant AS-cancer targets. …”
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Intervention effect and mechanism of Dracocephalum moldavica L. extract on bleomycin-induced pulmonary fibrosis in rats by Xiaoyu SUN, Li CHEN, Ruifang GAO, Hui YU, Min JIN

“…The disease targets related to pulmonary fibrosis were inquired using Gene Cards and DisGeNET. A protein-protein interaction (PPI) was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. …”
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Dietary protein intake and PM2.5 on ovarian cancer survival: A prospective cohort study by He-Li Xu, Yi-Fan Wei, Qi Bao, Ya-Li Wang, Xiao-Ying Li, Dong-Hui Huang, Fang-Hua Liu, Yi-Zi Li, Yue-Yang Zhao, Xin-Xin Zhao, Qian Xiao, Song Gao, Ren-Jie Chen, Ling Ouyang, Xia Meng, Xue Qin, Ting-Ting Gong, Qi-Jun Wu

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