Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress by Sadaf Sarwar, Adnan Sami, Muhammad Zeshan Haider, Layba Tasawar, Jannat Akram, Arsalan Ahmad, Muhammad Shafiq, Haitham E. M. Zaki, Gabrijel Ondrasek, Muhammad Shafiq Shahid

“…To identify their structural features, they employed phylogenetic analysis, protein interactions, localization, structure, miRNA targets, evolutionary analysis, and transcriptome studies. …”
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磷脂在蛋白质乳液中的作用研究进展Research progress on the role of phospholipids in protein-based emulsions by 李雪阳1，邹依彤1，涂向辉1，祁冰洁1，刘新2， 杨庆余1，王丽娟1 " LI Xueyang1, ZOU Yitong1, TU Xianghui1, QI Bingjie1, LIU Xin2 , YANG Qingyu1，WANG Lijuan1"

“…Proteins, as natural emulsifiers, are sensitive to environmental changes, and phospholipid-protein interactions can reduce the sensitivity of proteins to environmental changes. …”
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Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins by E. A. Antropova, T. M. Khlebodarova, P. S. Demenkov, A. S. Venzel, N. V. Ivanisenko, A.  D.  Gavrilenko, T.  V. Ivanisenko, A. V. Adamovskaya, P. M. Revva, I. N. Lavrik, V. A. Ivanisenko

“…The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. …”
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Noncoding RNA profiling in omentum adipose tissue from obese patients and the identification of novel metabolic biomarkers by Yongjiao Zhang, Yongjiao Zhang, Ao Chen, Ao Chen, Sumei Lu, Dong Liu, Xiaolei Xuan, Xiaofei Lei, Mingwei Zhong, Fei Gao

“…Subsequent analyses included functional annotation with GO and KEGG pathway mapping, validation via real-time quantitative polymerase chain reaction (qRT‒PCR), the exploration of protein‒protein interactions (PPIs), and the identification of key regulatory genes through network analysis.ResultsThe results indicated that, compared with those in healthy individuals, various lncRNAs, circRNAs, and miRNAs were significantly differentially expressed in obese subjects. …”
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Metformin blocks BIK1-mediated CPK28 phosphorylation and enhances plant immunity by Yazhou Bao, Qian Zhang, Hai Zhu, Yong Pei, Yaning Zhao, Yixin Li, Peiyun Ji, Dandan Du, Hao Peng, Guangyuan Xu, Xiaodan Wang, Zhiyuan Yin, Gan Ai, Xiangxiu Liang, Daolong Dou

“…Additionally, surface plasmon resonance (SPR) and microscale thermophoresis (MST) techniques were employed to identify MET targets. Protein-protein interactions were analyzed using a luciferase complementation assay and a co-immunoprecipitation assay. …”
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HPGCN: A graph convolutional network-based prediction model for herbal heat/cold properties by Qikai Niu, Jing’ai Wang, Hongtao Li, Lin Tong, Haiyu Xu, Weina Zhang, Ziling Zeng, Sihong Liu, Wenjing Zong, Siqi Zhang, Siwei Tian, Huamin Zhang, Bing Li

“…Based on protein-protein interactions (PPI) and herb-herb networks, 30 target genes were selected as features for herbal heat/cold property prediction. …”
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Tumor CEMIP drives immune evasion of colorectal cancer via MHC-I internalization and degradation by Ying Zhu, Jiao Li, Tao Zhang, Lei Zhao, Min Jin, Jinghua Ren, Jing Tang, Haihong Wang, Zhenyu Lin, Qing Liang, Ruiqi Li, Biying Zhang, Qingling Hua, Guojie Xu, Jiayuan Chen, Lanqing Wang, Dejun Zhang, Dandan Yu

“…Flow cytometry analysis was used to examine immune cells. Protein–protein interactions were investigated by co-immunoprecipitation and proximity ligation assays. …”
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Deciphering the functional roles of PE18 and PPE26 proteins in modulating Mycobacterium tuberculosis pathogenesis and immune response by Aquib Ehtram, Mohd Shariq, Neha Quadir, Neha Quadir, Salma Jamal, Manjunath Pichipalli, Sheeba Zarin, Sheeba Zarin, Javaid Ahmad Sheikh, Nasreen Z. Ehtesham, Seyed E. Hasnain, Seyed E. Hasnain

“…Despite their importance, the roles and molecular interactions of PE18 and PPE26 in Mtb pathogenesis require further investigation.MethodsWe explored the roles of PE18 and PPE26 using recombinant Mycobacterium smegmatis (Msmeg) as a model organism. Protein-protein interactions were analyzed biochemically to identify partners within the ESX-5 secretion system, including EspG5 and other PE/PPE proteins. …”
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Microcephaly protein ANKLE2 promotes Zika virus replication by Adam T. Fishburn, Cole J. Florio, Thomas N. Klaessens, Brian Prince, Neil A. B. Adia, Nicholas J. Lopez, Nitin Sai Beesabathuni, Sydney S. Becker, Liubov Cherkashchenko, Sophia T. Haggard Arcé, Vivian Hoang, Traci N. Shiu, R. Blake Richardson, Matthew J. Evans, Claudia Rückert, Priya S. Shah

“…We previously mapped ZIKV-host protein interactions and identified the interaction between ZIKV non-structural protein 4A (NS4A) and host microcephaly protein ankyrin repeat and LEM domain-containing 2 (ANKLE2). …”
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Elucidating the pharmacological foundations and mechanisms of the Sihai Shuyu formula in treating Graves’ disease through integrated serum metabolomics and network pharmacology wit... by Xiaoju Liu, Xingjia Li, Wenbin Huang, Yifan Cui, Fengyun Cheng, Guofang Chen, Guofang Chen, Xiaodong Mao, Chao Liu, Chao Liu, Shuhang Xu

“…A comprehensive analysis of the multi-level bioinformatic analysis, including protein-protein interactions (PPI) and functional pathways of the targets, was conducted, followed by verification through immunohistochemistry (IHC) to clarify SHSY’s pharmacological basis and action mechanisms in treating GD.ResultsAfter 8 weeks of treatment, SHSY significantly reduced serum T4 and TRAb levels in GD mice and enhanced the morphology of thyroid tissues. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…We utilised protein–protein interactions (PPIs), Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes to identify T2DM-associated MAFLD genes and potential mechanisms. …”
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Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes by Peter Vo, Denise M. Imai-Leonard, Benjamin Yang, Andrew Briere, Andy Shao, M. Isabel Casanova, David Adams, Takanori Amano, Oana Amarie, Zorana Berberovic, Lynette Bower, Robert Braun, Steve Brown, Samantha Burrill, Soo Young Cho, Sharon Clementson-Mobbs, Abigail D’Souza, Mary Dickinson, Mohammad Eskandarian, Ann M. Flenniken, Helmut Fuchs, Valerie Gailus-Durner, Jason Heaney, Yann Hérault, Martin Hrabe de Angelis, Chih-Wei Hsu, Shundan Jin, Russell Joynson, Yeon Kyung Kang, Haerim Kim, Hiroshi Masuya, Hamid Meziane, Steve Murray, Ki-Hoan Nam, Hyuna Noh, Lauryl M. J. Nutter, Marcela Palkova, Jan Prochazka, Miles Joseph Raishbrook, Fabrice Riet, Jennifer Ryan, Jason Salazar, Zachery Seavey, John Richard Seavitt, Radislav Sedlacek, Mohammed Selloum, Kyoung Yul Seo, Je Kyung Seong, Hae-Sol Shin, Toshihiko Shiroishi, Michelle Stewart, Karen Svenson, Masaru Tamura, Heather Tolentino, Uchechukwu Udensi, Sara Wells, Jacqueline White, Amelia Willett, Janine Wotton, Wolfgang Wurst, Atsushi Yoshiki, The International Mouse Phenotyping Consortium, Louise Lanoue, K. C. Kent Lloyd, Brian C. Leonard, Michel J. Roux, Colin McKerlie, Ala Moshiri

“…Phenotypes of human orthologues of mouse candidate genes were compared with known human CD genes to identify protein-protein interactions and molecular pathways using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Protein Analysis Through Evolutionary Relationships (PANTHER), and Kyoto Encyclopedia of Genes and Genomes. …”
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Optimasi Data Tidak Seimbang pada Interaksi Drug Target dengan Sampling dan Ensemble Support Vector Machine by Nabila Sekar Ramadhanti, Wisnu Ananta Kusuma, Annisa Annisa

“…This research is focusing on handling imbalanced data problem for drug-target (compound-protein) interaction data. There are many target protein and drug compound existed in compound-protein interaction databases, which many interactions are not validated yet by experiment. …”
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Immunoinformatics Approach for Multiepitope Vaccine Prediction from H, M, F, and N Proteins of Peste des Petits Ruminants Virus by Bothina B. M. Gaafar, Sumaia A. Ali, Khoubieb Ali Abd-elrahman, Yassir A. Almofti

“…For instance, the epitope 45MFLSLIGLL53 from the H protein interacted with four BoLA alleles, while 276FKKILCYPL284 predicted from the M protein interacted with two alleles. …”
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Potential Therapeutic Drugs for Parkinson’s Disease Based on Data Mining and Bioinformatics Analysis by Chuan Xu, Jiajun Chen, Xia Xu, Yingyu Zhang, Jia Li

“…Method differential gene candidates were obtained based on data mining of genes of PD brain tissue, original gene data analysis, differential gene crossover, pathway enrichment analysis, and protein interaction, and potential therapeutic drugs for Parkinson’s disease were obtained through drug-gene relationship. …”
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Network Pharmacology Analysis of the Therapeutic Potential of Colchicine in Acute Lung Injury by Fei Sun, Lijuan Zhang, Lulu Shen, Chunman Wang

“…We performed comprehensive pathway and process enrichment analyses on these genes. A protein-protein interaction network was constructed, and topological analysis was executed. …”
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Proteomic Characterization of Liver Cancer Cells Treated with Clinical Targeted Drugs for Hepatocellular Carcinoma by Hezhou Long, Jiafu Zhou, Changxia Zhou, Shuyu Xie, Jingling Wang, Minjia Tan, Junyu Xu

“…<b>Results</b>: Utilizing KEGG pathway enrichment analysis, biological process enrichment analysis, and protein interaction network analysis, we elucidated the common and specific metabolic pathways, biological processes, and protein interaction regulatory networks influenced by three liver cancer therapeutics. …”
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Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis by Yang C, Chen X, Liu J, Wang W, Sun L, Xie Y, Chang Q

“…Functional enrichment analyses, protein-protein interaction (PPI) analysis, and weighted gene co-expression network analysis (WGCNA) of the DEGs were performed. …”
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Naoxintong Is Involved in the Coagulation Regulation of Warfarin Through the MAPK Pathway by Luo X, Chen L, Xu J, Li J

“…Cytoscape software was applied to construct the “drug-target”network; the protein interaction network (PPI) was used to study the protein-protein interaction. …”
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Transcriptome analysis of muscle atrophy in Leizhou black goats: identification of key genes and insights into limb-girdle muscular dystrophy by Ke Wang, Mengning Xu, Xiaotao Han, Hu Liu, Jiancheng Han, Wei Sun, Hanlin Zhou

“…Protein interaction network analysis identified five key clusters related to muscle function and development. …”
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