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PhyloString: A web server designed to identify, visualize, and evaluate functional relationships between orthologous
Claudia Dorantes-Torres1, Maricela Carrera-Reyna1, Walter Santos1
1Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Plos One
|January 26, 2024
Summary
PhyloString visualizes protein functional networks across species. It identifies cohesive protein modules based on STRING database interactions and phylogenetic origins, aiding comparative analysis.
Area of Science:
- Bioinformatics
- Systems Biology
- Computational Biology
Background:
- Proteins are fundamental biological units with diverse functions (enzymatic, structural, regulatory).
- Understanding protein functional relationships is crucial for deciphering biological processes.
- Existing resources like the STRING database provide protein-protein interaction networks for model organisms.
Purpose of the Study:
- To develop a web server, PhyloString, for identifying and visualizing protein functional networks across different species.
- To enable the decomposition of these networks into cohesive modules based on interaction strength and phylogenetic origin.
- To facilitate comparative analysis of functional networks and protein modules across diverse organisms.
Main Methods:
- Utilized indices from the STRING database.
- Developed the PhyloString web server (https://biocomputo.ibt.unam.mx/phylostring/).
- Implemented a module decomposition strategy based on STRING interaction scores and phylogenetic data.
Main Results:
- Successfully developed and deployed the PhyloString web server.
- Demonstrated the identification and visualization of protein functional networks.
- Showcased the decomposition of networks into biologically relevant modules.
- Presented examples of functional networks and modules identified across different phylogenetic lineages.
Conclusions:
- PhyloString effectively facilitates the identification, visualization, and evaluation of protein functional networks and modules across diverse organisms.
- The module decomposition approach aids in understanding conserved and divergent protein interaction patterns.
- PhyloString serves as a valuable tool for comparative systems biology research.
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