Applications of domain-domain interactions in pathway study

Authors:
Ka-Lok Ng;Chien-Hung Huang;Hsueh-Chuan Liu;Hsiang-Chuan Liu
Affiliations:
Department of Bioinformatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung 413, Taiwan;Department of Computer Science and Information Engineering, National Formosa University, 64 Wen-Hwa Road, Hu-wei, Yun-Lin 632, Taiwan;Department of Bioinformatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung 413, Taiwan;Department of Bioinformatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung 413, Taiwan
Venue:
Computational Biology and Chemistry
Year:
2008

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Prediction of protein--protein interactions using random decision forest framework

Bioinformatics

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Abstract

The domain combination pair approach is employed to derive putative protein domain-domain interactions (DDI) from the protein-protein interactions (PPI) database DIP. The results of putative DDI are computed for seven species. To determine the prediction performance, putative DDI results are compared with that of the database InterDom, where an average matching ratio of about 76% can be achieved. Several real PPI pathways are reconstructed based on the predicted DDI results. It is found that the pathways could be reconstructed with reasonable accuracy. Furthermore, a novel quantity, so called AP-order index, is introduced to predict the regulatory order for six PPI pathways. It is found that the AP-order index is a very reliable parameter to determine the regulatory order of PPI.