Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana

BACKGROUND: Many essential cellular processes, such as cellular metabolism, transport, cellular metabolism and most regulatory mechanisms, rely on physical interactions between proteins. Genome-wide protein interactome networks of yeast, human and several other animal organisms have already been established, but this kind of network reminds to be established in the field of plant. RESULTS: We first predicted the protein protein interaction in Arabidopsis thaliana with methods, including ortholog, SSBP, gene fusion, gene neighbor, phylogenetic profile, coexpression, protein domain, and used Naïve Bayesian approach next to integrate the results of these methods and text mining data to build a genome-wide protein interactome network. Furthermore, we adopted the data of GO enrichment analysis, pathway, published literature to validate our network, the confirmation of our network shows the feasibility of using our network to predict protein function and other usage. CONCLUSIONS: Our interactome is a comprehensive genome-wide network in the organism plant Arabidopsis thaliana, and provides a rich resource for researchers in related field to study the protein function, molecular interaction and potential mechanism under different conditions.