Reconstructing protein-protein interaction networks from domain-domain interactions

[[abstract]]Protein-protein interactions (PPIs) play pivotal roles in various aspects of the structural and functional organization of the cell, and their complete description is indispensable to thorough understanding of the cell. Currently, domain-domain interactions can be useful for validating, annotating, and predicting protein-protein interactions. In this study, we employ the domain combination pair approach, introduced by Han et. al [1,2] to derive putative protein domain-domain interactions from the protein-protein interaction database DIP. Domain annotation of each protein-protein interaction record in DIP is obtained from the protein domain database, Pfam.The results of putative domain-domain interaction by Han et al. was extended to seven species (C.elegan, D.melanogaster, E.coli, H.pylori, H.sapiens, M.musculus and S.cerevisiae). According to former basis, we offer an ordering method protein-portein interactions to predict the ordering relationship. We use an ordering index(OI) combined to analyze data[7,8], and we use the ordering index to predict the association of proteins through the dynamics of protein expression. All results are available at http://210.70.80.163/kzbio2/index.ph