MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data by V. G. Levitsky, A. V. Tsukanov, T. I. Merkulova

“…The multiprotein complex mapped in a ChIP-seq experiment includes target and other “partner” TFs linked by protein-protein interactions. Not all these TFs bind to DNA directly. …”
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Construction of Shoot Apical Meristem cDNA Yeast Library of <i>Brassica napus</i> L. and Screening of Proteins That Interact with the Inflorescence Regulatory Factors BnTFL1s by Lingxiong Zan, Haidong Liu, Xutao Zhao, Dezhi Du, Kaixiang Li

“…The recombination efficiency of the yeast two-hybrid (Y2H) library that we constructed was 100%, with insertion fragment lengths ranging from 750 to 2000 bp and a capacity of approximately 1.44 × 10⁷ CFUs (colony-forming units), sufficient for screening protein interactions. Additionally, the bait vector pGBKT7-BnTFL1s was transformed into yeast cells alongside positive and negative controls, demonstrating no toxicity to the yeast cells and no self-activation. …”
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In silico analysis of SNPs and miRNAs of KCTD13, CSDE1, SLC6A1 genes associated with autism spectrum disorder by Kübra Çoruh Kınalı, Ebru Özkan Oktay, Mesut Karahan

“…GeneMANIA and STRING were also employed to explore gene–gene and protein–protein interactions. Results A total of 16 variants in these three genes were estimated to be potentially harmful via in silico analysis. …”
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REVIEW ON PROTEIN FOOTPRINTING AS A TOOL IN STRUCTURAL BIOLOGY by Oluwatosin Ogundairo, Oluwatoyin Ayo-Farai, Chinedu Paschal Maduka, Chiamaka Chinaemelum Okongwu, Abdulraheem Olaide Babarinde, Olamide Sodamade

“…The application of protein footprinting in studying protein-protein interactions, ligand binding, and conformational changes is highlighted through a detailed examination of key studies and experimental approaches. …”
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Quantitative proteomic studies of the intestinal mucosa provide new insights into the molecular mechanism of ulcerative colitis by Yandong Guo, Dahal Pabitra, Lei Pan, Lanbo Gong, Aimin Li, Side Liu, Jing Xiong

“…Network analysis showed that proteins were involved in 4 pathways in UC-I and 3 pathways in UC-N tissues, and participated in protein-protein interactions. Increased expression of 9 DEPs, including TXNDC5, EPX, and ITGAM were detected in UC patients compared to normal control subjects. …”
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Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies by A. N. Chikaev, A. P. Rudometov, Yu. A. Merkulyeva, L. I. Karpenko

“…Despite being a fairly old method, phage display is still widely used for studying protein-protein, peptide-protein and DNA-protein interactions due to its relative simplicity and versatility. …”
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Distinct subcellular localization of tau and alpha-synuclein in lewy body disease by D. Luke Fischer, Marissa Menard, Omar Z. Abdelaziz, Nicholas M. Kanaan, Virginia G. Cobbs, Richard E. Kennedy, Geidy E. Serrano, Thomas G. Beach, Laura A. Volpicelli-Daley

“…The relationship between tau and α-syn copathology is important for explaining clinical symptoms, severity, and progression, but there is no evidence for frequent, direct protein-protein interactions in the middle temporal gyrus.…”
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Post-Translational Modifications of Proteins Orchestrate All Hallmarks of Cancer by Pathea Shawnae Bruno, Aneeta Arshad, Maria-Raluca Gogu, Natalie Waterman, Rylie Flack, Kimberly Dunn, Costel C. Darie, Anca-Narcisa Neagu

“…All cancer hallmarks develop due to PTMs of proteins, which modulate gene transcription, intracellular and extracellular signaling, protein size, activity, stability and localization, trafficking, secretion, intracellular protein degradation or half-life, and protein–protein interactions (PPIs). PTMs associated with cancer can be exploited to better understand the underlying molecular mechanisms of this heterogeneous and chameleonic disease, find new biomarkers of cancer progression and prognosis, personalize oncotherapies, and discover new targets for drug development.…”
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siRNA-mediated inhibition of hTERT enhances the effects of curcumin in promoting cell death in precursor-B acute lymphoblastic leukemia cells: an in silico and in vitro study by Muhammad Hossein Ashoub, Ali Afgar, Alireza Farsinejad, Razieh Razavi, Samira Anvari, Ahmad Fatemi

“…Molecular docking revealed strong curcumin-protein interactions (∆G = -34.24 kcal/mol for hTERT). This study establishes hTERT as a critical regulator of ferroptotic cell death in pre-B ALL, operating through redox homeostasis, iron metabolism, and lipid peroxidation pathways. …”
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A multi-dimensional validation strategy of pharmacological effects of Radix Isatidis Mixtures against the co-infection of Mycoplasma gallisepticum and Escherichia coli in poultry by Xiaodi Jin, Jinhai Huo, Yecheng Yao, Rui Li, Mengqing Sun, Jichang Li, Zhiyong Wu

“…To further demonstrate the various mechanisms underlying the pharmacological effects of RIM, we conducted a validation study focusing on gene expression, protein interactions, metabolic pathways, and molecular docking. …”
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Genetic and Plasma Proteomic Approaches to Identify Therapeutic Targets for Graves&rsquo; Disease and Graves&rsquo; Ophthalmopathy by Ke C, Yu Y, Li J, Yu Y, Sun Y, Wang Y, Wang B, Lu Y, Tang M, Wang N, Chen Y

“…Then, downstream analyses were performed to detect protein interactions, gene function, cell type-specific expression and druggable information.Results: This study genetically predicted levels of 62 plasma proteins were associated with GD risk. …”
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Differential expressed genes (DEGs) and differential alternative splicing genes (DASs) revealed the common pathologic mechanism of three bacterial pathogens to American eels (Angui... by Zihao Chen, Guanghua Sun, Songlin Guo

“…Finally, the analysis of protein-protein interactions identified 72 out of 332 common DASs. …”
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Tyrosine hydroxylase of the brain and it’s regulation by glucocorticoids by E. V. Sukhareva, T. S. Kalinina, V. V. Bulygina, N. N. Dygalo

“…However, despite optimistic claims made the classical GRE was not found in the TH gene promoter. Protein – protein interactions between hormone-activated GR and other transcription factors, for example, AP-1, provide an additional mechanism for the effects of glucocorticoids on gene expression. …”
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Functional Characterization of the SHIP1-Domains Regarding Their Contribution to Inositol 5-Phosphatase Activity by Spike Murphy Müller, Nina Nelson, Manfred Jücker

“…The Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) is a multidomain protein consisting of two protein–protein interaction domains, the Src homology 2 (SH2) domain, and the proline-rich region (PRR), as well as three phosphoinositide-binding domains, the pleckstrin homology-like (PHL) domain, the 5-phosphatase (5PPase) domain, and the C2 domain. …”
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Mining Potential Drug Targets and Constructing Diagnostic Models for Heart Failure Based on miRNA-mRNA Networks by Xiangming Fang, Rensheng Song, Jiaxing Wei, Qin Liao, Zhenhong Zeng

“…Subsequently, gene set enrichment analysis and annotation were performed using WebGestaltR package. Protein-protein interactions were identified using the STRING database. …”
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Dual role of Cathepsin S in cutaneous melanoma: insights from mendelian randomization and bioinformatics analysis by Linsa Zhou, Qiang Zhou, Qian Guo, Peng Lai, Chen Rui, Wanqing Li, Xuemei Chen, Yue Zhuo, Xiaoping Zhong, Sen Lin

“…Finally, the role of target genes in CM was revealed by pan-cancer analysis, expression and immune-infiltration evaluations, immuno-checking targeting analysis, immunotherapy response analysis, survival analysis, and protein-protein interactions (PPI) network and enrichment analyses. …”
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Harnessing the power of proteins in modulation of miRNAs for targeting Iron deficiency Anemia: Opinion for future implications and strategies by Ray Wagiu Basrowi, Ray Wagiu Basrowi, Ray Wagiu Basrowi, Tonny Sundjaya, Tonny Sundjaya, Dessy Pratiwi, Nurlinah Amalia, Nurlinah Amalia, Nurlinah Amalia, Yosi Yohanes Putra Tandi, Muhammad Yasir Syafa’atulloh, Garuda Nusantara Putra Utomo, Muhammad Abdir Rahman Albarok, Fahrul Nurkolis

“…Our synthesis highlights key molecular mechanisms: miR-15a suppresses erythropoiesis by inhibiting c-Myb, miR-24 impairs heme biosynthesis through ALK4 regulation, while miR-150 and miR-223 modulate critical hematopoietic pathways affecting cell differentiation and apoptosis. These miRNA-protein interactions suggest targeted therapies such as protein-based miRNA modulators could optimize erythropoiesis, advancing IDA management. …”
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Genetic variation reveals the therapeutic potential of BRSK2 in idiopathic pulmonary fibrosis by Zhe Chen, Mingyang Tang, Nan Wang, Jiangjiang Liu, Xiaoyan Tan, Haitao Ma, Jing Luo, Kai Xie

“…PheWAS revealed no significant drug-related toxicities for BRSK2, and its therapeutic potential was further underscored by protein interaction analyses. Conclusions BRSK2 is identified as a critical pathogenic factor in IPF, with strong potential as a therapeutic target. …”
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Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics by George S. Biggs, Emma E. Cawood, Aini Vuorinen, William J. McCarthy, Harry Wilders, Ioannis G. Riziotis, Antonie J. van der Zouwen, Jonathan Pettinger, Luke Nightingale, Peiling Chen, Andrew J. Powell, David House, Simon J. Boulton, J. Mark Skehel, Katrin Rittinger, Jacob T. Bush

“…In this study, 80 reactive fragments were screened in two cell lines identifying >400 ligand-protein interactions. Hits were validated through concentration-response experiments and the platform was utilised for hit expansion and live cell experiments. …”
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Comprehensive bioinformatics analysis identifies hub genes associated with immune cell infiltration in early-onset schizophrenia by Shasha Wu, Tailian Xue, Yilin Li, Weikang Chen, Yan Ren

“…Hub genes were identified through protein-protein interactions (PPIs) and the GeneMANIA database. The diagnostic potential of immune-associated hub genes was evaluated using ROC analysis. …”
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