Supplementary Data for "Computational Prediction of Host-Pathogen Protein-Protein Interactions"


Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral


Dyer, M. D., T. M. Murali, and B. W. Sobral. (2007). Computational prediction of host-pathogen protein-protein interactions. Bioinformatics 27:i159-i166.


We present a method that integrates known intra-species PPIs with protein domain profiles to predict PPIs between host and pathogen proteins. Given a set of intra-species PPIs, we identify the functional domains in each of the interacting proteins. For every pair of functional domains, we use Bayesian statistics to assess the probability that two proteins with that pair of domains will interact. We apply our method to the Homo sapiens - Plasmodium falciparum host-pathogen system. Our system predicts 516 PPIs between proteins from these two organisms. We show that human protein pairs we predict to interact with the same Plasmodium protein are close to each other in the human PPI network and that Plasmodium pairs predicted to interact with same human protein are co-expressed in DNA microarray datasets measured during various stages of the Plasmodium life cycle. Finally, we identify functionally enriched sub-networks spanned by the predicted interactions and discuss the plausibility of our predictions.


File Description Links
Tab-delimited files of predicted protein-protein interactions. Files contain UniProt ids and predicted probabilities. human-Plasmodium
Tab-delimited files of enriched Gene Ontology functions among predicted interactions for the human-Plasmodium system. There were no enriched functions for the fly-Plasmodium system. human-Plasmodium
Tab-delimited files of all protein-protein interactions used in the training step of this study. These files contain UniProt ids. Human
Tab-delimited files of proteins considered during the prediction step of this study. These files contain UniProt ids. Human