Title of article :
Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis
Author/Authors :
Leong, Geok Wei Universiti Teknologi Malaysia - Faculty of Biosciences and Medical Engineering - Department of Biotechnology and Medical Engineering, Malaysia , Lee, Sheau Chen Universiti Teknologi Malaysia - Faculty of Biosciences and Medical Engineering - Department of Biotechnology and Medical Engineering, Malaysia , Lau, Cher Chien Universiti Teknologi Malaysia - Faculty of Biosciences and Medical Engineering - Department of Biotechnology and Medical Engineering, Malaysia , Klappa, Peter Universiti Teknologi Malaysia - Faculty of Biosciences and Medical Engineering - Department of Biotechnology and Medical Engineering, Malaysia , Shamsir, Mohd Shahir Universiti Teknologi Malaysia - Faculty of Biosciences and Medical Engineering - Department of Biotechnology and Medical Engineering, Malaysia
Abstract :
Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out so far. In this study, we compare seven commonly used visualization tools, based on input and output file format, layout algorithm, database integration, Gene Ontology annotation and accessibility of each tool. The assessment was carried out based on brain disease datasets. Our suggested tools, NAViGaTOR, Cytoscape and Gephi perform competitively as PPI network visualization tools, can be a reference for future researches on PPI mapping and analysis.
Keywords :
Visualization tools , protein , protein interaction network , system biology , proteomic database , protein mining , protein mapping
Journal title :
Jurnal Teknologi :F
Journal title :
Jurnal Teknologi :F
