Computational Molecular Biology 2024, Vol.14, No.5, 191-201 http://bioscipublisher.com/index.php/cmb 194 4.3 Bioinformatics tools and databases for PPI analysis The utilisation of bioinformatics tools and databases is a fundamental aspect of the analysis and visualisation of PPI networks. STRING is a database of known and predicted PPIs that integrates data from a variety of sources, including experimental data, computational prediction methods, and public text collections. It offers a comprehensive overview of protein interactions and is widely utilized tool in the field of PPI network analysis (Zainal-Abidin et al., 2022). CYTOSCAPE is an open-source software platform designed for the visualisation of complex networks and the integration of diverse attribute data. It is particularly useful for visualizing PPI networks and the subsequent analysis of their topological properties (Figure 1) (Zainal-Abidin et al., 2022). GO analysis is a method of categorizing proteins within PPI network based on their biological processes, cellular components, and molecular functions. This approach was employed to identify drought-responsive proteins in rice (Hamzelou et al., 2020). By integrating experimental data with bioinformatics tools, researchers can construct detailed PPI networks that provide insights into the molecular mechanisms underlying drought stress responses in rice. The networks can be employed to identify potential targets for genetic improvement and breeding programs, with the objective of enhancing drought tolerance in rice. Figure 1 Bioinformatics workflow for the construction of protein–protein interaction network (PPI) (Adopted from Zainal-Abidin et al., 2022) 5 Insights from Proteomics and Bioinformatics Analysis 5.1 Identification of key drought-responsive proteins in rice Proteomic studies have identified a number of key proteins that respond to drought stress in rice. For example, a study of diverse rice genotypes demonstrated that eight proteins were consistently induced across all genotypes under drought conditions, indicating their potential role in drought tolerance mechanisms (Hamzelou et al., 2020). Furthermore, the overexpression of specific proteins such as late embryogenesis abundant (LEA) proteins, has been demonstrated to enhance drought resistance in rice, thereby underscoring their pivotal role in stress response (Xiao et al., 2007). Another study identified 38 co-upregulated proteins related to drought tolerance in weedy rice, with six proteins exhibiting a significant association with drought tolerance (Han et al., 2020). These findings highlight the significance of these proteins in enhancing drought resilience in rice.
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