Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis

Authors

  • Geok Wei Leong Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
  • Sheau Chen Lee Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
  • Cher Chien Lau Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
  • Peter Klappa University of Kent, UK
  • Mohd Shahir Shamsir Omar Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia

DOI:

https://doi.org/10.11113/jt.v63.1226

Keywords:

Visualization tools, protein-protein interaction network, system biology, proteomic database, protein mining, protein mapping

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.

 

References

Falgueras, J., Lara, A., Fernandez-Pozo, N. et al. 2010. SeqTrim: A High-throughput Pipeline for Pre-processing any Type of Sequence Read. BMC Bioinformatics. 11: 38.

Gaulton, A., Overington, J. P. 2010. Role of Open Chemical Data in Aiding Drug Discovery and Design. Future Medicinal Chemistry. 2: 903–907.

Batagelj, V., Mrvar, A. 1998. Pajek - Program for Large Network Analysis. Connections. 21: 47–57.

Shannon, P., Markiel, A., Ozier, O. et al. 2003. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res. 13: 2498–2504.

Enright, A. J., Ouzounis, C. A. 2001. BioLayout-an Automatic Graph Layout Algorithm for Similarity Visualization. Bioinformatics. 17: 853–854.

Brown, K. R., Otasek, D., Ali, M. et al. 2009. NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Bioinformatics. 25: 3327–3329.

Gehlenborg, N., O'Donoghue, S. I., Baliga, N. S. et al. 2010. Visualization of Omics Data for Systems Biology. Nat Methods. 7: S56–68.

Pavlopoulos, G., Wegener, A-L., Schneider, R. A. 2008. Survey of Visualization Tools for Biological Network Analysis. BioData Mining. 1: 12.

Suderman, M., Hallett, M. 2007. Tools for Visually Exploring Biological Networks. Bioinformatics. 23: 2651–2659.

The Gene Ontology Consortium. 2000. Gene Ontology: Tool for the Unification of Biology. Nat Genet. 25: 25–29.

Hernandez-Toro, J., Prieto, C., De Las Rivas, J. 2007. APID2NET: Unified Interactome Graphic Analyzer. Bioinformatics. 23: 2495–2497.

Aranda B, Achuthan P, Alam-Faruque Y et al. 2009. The IntAct Molecular Interaction Database in 2010. Nucleic Acids Research. 38 (Database issue): D525–31.

Bader, G. D., Donaldson, I., Wolting, C. et al. 2001. BIND--The Biomolecular Interaction Network Database. Nucl. Acids Res. 29: 242–245.

Zanzoni, A., Montecchi-Palazzi, L., Quondam, M. et al. 2002. MINT: a Molecular INTeraction Database. FEBS Letters. 513: 135–140.

Stark, C., Breitkreutz, B-J., Reguly, T. et al. 2006. BioGRID: a General Repository for Interaction Datasets. Nucl. Acids Res. 34: D535–539.

Breitkreutz, B-J., Stark, C., Reguly, T. et al. 2008. The BioGRID Interaction Database: 2008 Update. Nucl. Acids Res. 36: D637–640.

Xenarios, I., Salwinski, L., Duan, X. J. et al. 2002. DIP, the Database of Interacting Proteins: A Research Tool for Studying Cellular Networks of Protein Interactions. Nucl. Acids Res. 30: 303–305.

Keshava Prasad, T. S., Goel, R., Kandasamy, K. et al. 2009. Human Protein Reference Database-2009 Update. Nucl. Acids Res. 37: D767–772.

Fruchterman, T. M. J., Reingold, E. M. 1991. Graph Drawing by Force-directed Placement. Softw. Pract. Exper. 21: 1129–1164.

Han, K., Ju, B-H. A 2003. Fast Layout Algorithm for Protein Interaction Networks. Bioinformatics. 19: 1882–1888.

Downloads

Published

2013-07-11

Issue

Section

Science and Engineering

How to Cite

Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis. (2013). Jurnal Teknologi (Sciences & Engineering), 63(1). https://doi.org/10.11113/jt.v63.1226