Applications of domain-domain interactions in pathway study.
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.
Ng
Ka-Lok
KL
Department of Bioinformatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung 413, Taiwan.
Huang
Chien-Hung
CH
Liu
Hsueh-Chuan
HC
Liu
Hsiang-Chuan
HC
D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D030562:Databases, Protein; D008954:Models, Biological; D011237:Predictive Value of Tests; D054730:Protein Interaction Domains and Motifs / Q000502:physiology*; D025941:Protein Interaction Mapping / Q000379:methods* / Q000706:statistics & numerical data; D015398:Signal Transduction / Q000502:physiology*; D013045:Species Specificity