Genome-wide characterization of the MADS-box gene family in Paeonia ostii and expression analysis of genes related to floral organ development by Xueting Yang, Qi Guo, Shaodan Liu, Duoduo Wang, Dingding Zuo, Tongfei Niu, Dongfeng Wei, Lili Guo, Xiaogai Hou

“…We additionally created protein‒protein interaction networks for PoMADS proteins and analysed proteins that could interact among PoMADSs in Arabidopsis thaliana and grape. …”
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Analysis of diagnostic genes and molecular mechanisms of Crohn’s disease and colon cancer based on machine learning algorithms by Jie Xiao, Junyao Liang, Tao Zhou, Man Zhou, Dexu Zhang, Hui Feng, Chusen Tang, Qian Zhou, Weiqing Yang, Xiaoqin Tan, Wanjia Zhang, Yin Xu

“…Weighted Gene Co-expression Network Analysis (WGCNA), differentially expressed genes (DEGs), and protein-protein interaction (PPI) network analysis were conducted. …”
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Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins by Kazuma Yoshioka, Reiko Nakagawa, Chi Lieu Kim Nguyen, Hayate Suzuki, Kiyohiro Ishigaki, Seiya Mizuno, Tsukasa Okiyoneda, Shizufumi Ebihara, Kazuya Murata

“…Here we employed a proximity‐dependent biotinylation approach to characterize the USP46 protein interaction partners. Using homology‐independent targeted integration (HITI), a genome editing technique, we established knockin cell lines that stably express USP46 wildtype‐ or ΔK92‐biotin ligase fusion protein. …”
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In silico evaluation of missense SNPs in cancer-associated Cystatin A protein and their potential to disrupt Cathepsin B interaction by Shafaat Hossain, Omar Hamza Bin Manjur, Mst Sharmin Sultana Shimu, Tamanna Sultana, Mustafizur Rahman Naim, Shahariar Siddique, Abdullah Al Mamun, Md Miftaur Rahman, Md Abu Saleh, Md Rakibul Hasan, Tania Rahman

“…Five mutations (Y43C, Y43N, V48F, Y53H, and E94K) located in the conserved region were found to be highly deleterious and less stabilizing. The protein-protein interaction network found that Cathepsin B (CTSB) interacts highly with CSTA. …”
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Inhibition of anti-tumour reactivity of immune cells in the salivary gland cancer: A proteomic approach by Rajdeep Chakraborty, Charbel Darido, Aidan Tay, Thiri Zaw, Shoba Ranganathan, Fei Liu, Giuseppe Palmisano

“…We performed SWATH, proteome profilers, gene ontology biological function, functional annotation clustering and protein interaction network analysis of all cancer samples in the co-culture models. …”
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Tryptophan metabolism-related gene CYP1B1 serves as a shared biomarker for both Parkinson’s disease and insomnia by Xin-Yu Li, Wen-Kai Yu, Jing-Hao Wu, Wen-Jun He, Yu-Nan Cheng, Kai Gao, Yi-Han Wei, Yu-Sheng Li

“…Through Protein–Protein Interaction (PPI) network analysis, Support Vector Machine-Recursive Feature Elimination (SVM-RFE) , and Extreme Gradient Boosting (XGBoost) machine learning, we identified Cytochrome P4501B1 (CYP1B1) and Electron Transfer Flavoprotein Alpha (ETFA) as key hub genes. …”
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Identification of circRNA/miRNA/mRNA regulatory network involving (+)-catechin ameliorates diabetic nephropathy mice by Chao Chen, Dina Zhu, Shuai Zhang, Wensheng Zhang

“…The expanded network of proteins interacting with these 5 genes shows that the TGF-β signaling pathway, signaling pathways regulating pluripotency of stem cell, fat digestion and absorption, and PPAR signaling pathway was highly enriched. …”
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Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy by Akram Yazdani, Heinz-Josef Lenz, Gianluigi Pillonetto, Raul Mendez-Giraldez, Azam Yazdani, Hanna Sanoff, Reza Hadi, Esmat Samiei, Alan P. Venook, Mark J. Ratain, Naim Rashid, Benjamin G. Vincent, Xueping Qu, Yujia Wen, Michael Kosorok, William F. Symmans, John Paul Y. C. Shen, Michael S. Lee, Scott Kopetz, Andrew B. Nixon, Monica M. Bertagnolli, Charles M. Perou, Federico Innocenti

“…An external cohort of paired CRC normal and tumor samples, along with protein-protein interaction databases, was used for replication. …”
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DET induces apoptosis and suppresses tumor invasion in glioma cells via PI3K/AKT pathway by Rui Zhao, Mengran Wang, Zeyu Wu, Panpan Zhao, Huiling Dong, Yue Su, Chenghui Zhao, Min Qi, Shizhang Ling, Shizhang Ling, Xiaochun Jiang, Xiaochun Jiang

“…GBM-related targets were obtained through multi-omics approaches. A protein-protein interaction (PPI) network was constructed using Cytoscape and STRING, and target binding was evaluated through molecular docking. …”
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Exploration of interstitial fluid proteome in Homo sapiens forearm through a cutting edge intradermal microdialysis and high-throughput proteomics approach: a pilot study by Yu Sakamoto, Naoto Fujii, Junko Shibato, Ravi Gupta, Cheol Woo Min, Sun Tae Kim, Ranjith Kumar Bakku, Randeep Rakwal

“…Dialysate samples were checked for protein extracted in LB-TT, SDS-PAGE, and by LC–MS/MS. A protein–protein interaction (PPI) network was constructed with genes from STRING using Cytoscape. …”
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CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics by Young-Kyu Park, Tae-Wook Kang, Su-Jin Baek, Kwon-Il Kim, Seon-Young Kim, Doheon Lee, Yong Sung Kim

“…The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. …”
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Systematic free energy insights into the enhanced dispersibility of myofibrillar protein in low-salt solutions through ultrasound-assisted enzymatic deamidation by Yating Liu, Zongyun Yang, Zhen Li, Juan Shen, Xia Wang, Ru Li, Ye Tao, Xinglian Xu, Peng Wang

“…Our research contributed to the improvement of the colloidal dispersibility of MPs under low-salt conditions and the regulation of protein interaction by ultrasound assistance.…”
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Bioinformatics and System Biological Approaches for the Identification of Genetic Risk Factors in the Progression of Cardiovascular Disease by Joy Dip Barua, Shudeb Babu Sen Omit, Humayan Kabir Rana, Nitun Kumar Podder, Utpala Nanda Chowdhury, Md Habibur Rahman

“…We performed several analyses including gene expression analysis, diseasome analysis, protein-protein interaction (PPI) analysis, and pathway analysis for discovering the relationship between CVD and its risk factors. …”
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The role of SASP in ischemic stroke: a deep dive into cellular mechanisms by Dong Xie, Yang Liu, Fang-Biao Xu, Jin-Sheng Zhang

“…The present study endeavored to preliminarily dissect the SASP-IS nexus via combined bulk and single-cell transcriptome analysis.MethodsAggregated expression profiles from human peripheral blood bulk chips and MCAO mouse single-cell sequencing data, followed by SASP gene analysis. Executed protein interaction network and enrichment assays. Investigated immune infiltration in stroke patients, managed quality control and annotation of single-cell data, cherry-picked central cells based on SASP scores, unearthed essential genes via enrichment analysis, conducted pseudo-time and intercellular communication studies, and prognosticated drugs for hub genes. …”
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CDC25B Is a Prognostic Biomarker Associated With Immune Infiltration and Drug Sensitivity in Hepatocellular Carcinoma by Zixiang Huang, Liangzhi Xu, Zhengqiang Wu, Xiaofeng Xiong, Linfei Luo, Zhili Wen

“…Gene set enrichment analysis (GSEA) was used to identify signaling pathways enriched in CDC25B expression, and differential genes (DEGs) were used to screen out coexpressed hub genes and construct protein-protein interaction (PPI) networks. 5-Ethynyl-2′-deoxyuridine (EDU) staining was used to compare the proliferation and differentiation ability of the HCC cell line (HCC-LM3) after knockdown of CDC25B. …”
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Effects of Baicalin on Gout Based on Network Pharmacology, Molecular Docking, and in vitro Experiments by Liu C, Liu W, Lu H, Fan Y, Wang A

“…Then, the potential targets and signaling pathways were acquired via protein–protein interaction (PPI), as well as the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. …”
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Anti-lung Cancer Mechanism of Quercetin Based on Network Pharmacology and Experimental Validation by Yi WANG, Xiaofang PU

“…Target mapping was performed to identify the targets of quercetin in treating NSCLC. The protein-protein interaction (PPI) network was obtained from the STRING database and analyzed using Cytoscape 3.7.2 for visualization. …”
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Transcriptomic Analysis of Pathogenicity Genes in Sclerotinia sclerotiorum Affecting Brassica napus by Hengameh Taheri, Mohamad Hamed Ghodoum Parizipour

“…It examines these genes' codon usage bias (CUB) to find the optimal codons effective in gene expression and the factors effective in the formation of CUB. Protein-protein interaction network was drawn and several hub genes were determined and ranked according to the CytoHubba tool among which the genes encoding nitrate reductase, beta-glucosidase, glucanase, PA14 domain-containing protein, carbohydrate-binding module family 1, and acyl-coenzyme A oxidase were found to be associated with the SSR induction. …”
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Bioinformatics analysis combined with experimental validation reveals the biological role of the ILK gene in prostate cancer by Xiao-xiang Yu, Yi Liu, Rong-jiang Luo, Zi-xuan Song, Wen-kai Chen, Zeng-mi Mo, Feng-jing Wang

“…Results 544 significant genes were identified by WGCNA. The protein–protein interaction (PPI) network analysis revealed that MYC was the central regulatory gene, with the intersected genes mainly involved in regulating cell adhesion and drug metabolism in prostate cancer (PCa). …”
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Identification of key genes associated with oxidative stress in ischemic stroke via bioinformatics integrated analysis by Gaiyan Li, Yu Cheng, Shanshan Ding, Qianyun Zheng, Lanqiong Kuang, Ying Zhang, Ying Zhou

“…Subsequently, protein–protein interaction (PPI) network and machine learning algorithms were utilized to excavate feature genes. …”
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