Universiti Teknologi Malaysia Institutional Repository

Comparison of computational tools for protein-protein interaction (PPI) mapping and analysis

Geok, Wei Leong and Sheau, Chen Lee and Cher, Chien Lau and Klappa, Peter and Shamsir, Mohd. Shahir (2013) Comparison of computational tools for protein-protein interaction (PPI) mapping and analysis. Jurnal Teknologi (Science & Engineering), 63 (1). pp. 1-8. ISSN E–ISSN 2180–3722

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Official URL: https://dx.doi.org/10.11113/jt.v63.1226


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.

Item Type:Article
Uncontrolled Keywords:visualization tools, protein-protein interaction network, system biology, protein mining, protein mapping
Subjects:Q Science > QH Natural history > QH301 Biology
Divisions:Biosciences and Medical Engineering
ID Code:33543
Deposited By: Norhayati Abu Ruddin
Deposited On:28 Aug 2013 07:41
Last Modified:27 Sep 2018 07:06

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