ppiPre: predicting protein-protein interactions by combining heterogeneous features

Background: Protein-protein interactions (PPIs) are crucial in cellular processes. Since the current biological experimental techniques are time-consuming and expensive, and the results suffer from the problems of incompleteness and noise, developing computational methods and software tools to predict PPIs is necessary. Although several approaches have been proposed, the species supported are often limited and additional data like homologous interactions in other species, protein sequence and protein expression are often required. And predictive abilities of different features for different kinds of PPI data have not been studied. Results: In this paper, we propose ppiPre, an open-source framework for PPI analysis and prediction using a combination of heterogeneous features including three GO-based semantic similarities, one KEGG-based co-pathway similarity and three topology-based similarities. It supports up to twenty species. Only the original PPI data and gold-standard PPI data are required from users. The experiments on binary and co-complex gold-standard yeast PPI data sets show that there exist big differences among the predictive abilities of different features on different kinds of PPI data sets. And the prediction performance on the two data sets shows that ppiPre is capable of handling PPI data in different kinds and sizes. ppiPre is implemented in the R language and is freely available on the CRAN (http://cran.r-project.org/web/packages/ppiPre/). Conclusions: We applied our framework to both binary and co-complex gold-standard PPI data sets. The detailed analysis on three GO aspects suggests that different GO aspects should be used on different kinds of data sets, and that combining all the three aspects of GO often gets the best result. The analysis also shows that using only features based solely on the topology of the PPI network can get a very good result when predicting the co-complex PPI data. ppiPre provides useful functions for analysing PPI data and can be used to predict PPIs for multiple species.