LocFuse: Human protein–protein interaction prediction via classifier fusion using protein localization information

• Published in: Genomics (San Diego, Calif.) Calif.), 2014-12, Vol.104 (6), p.496-503
• Main Authors: Zahiri, Javad, Mohammad-Noori, Morteza, Ebrahimpour, Reza, Saadat, Samaneh, Bozorgmehr, Joseph H., Goldberg, Tatyana, Masoudi-Nejad, Ali
• Format: Article
• Language: English
• Subjects: Artificial Intelligence; Cellular localization; Classifier fusion; Ensemble learning; Humans; Machine learning; Metabolomics - methods; Protein Binding; Protein Processing, Post-Translational; Protein Transport; Protein–protein interaction; Proteome - metabolism; Proteomics - methods; Software
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2014.10.006

Protein–protein interaction (PPI) detection is one of the central goals of functional genomics and systems biology. Knowledge about the nature of PPIs can help fill the widening gap between sequence information and functional annotations. Although experimental methods have produced valuable PPI data, they also suffer from significant limitations. Computational PPI prediction methods have attracted tremendous attentions. Despite considerable efforts, PPI prediction is still in its infancy in complex multicellular organisms such as humans. Here, we propose a novel ensemble learning method, LocFuse, which is useful in human PPI prediction. This method uses eight different genomic and proteomic features along with four types of different classifiers. The prediction performance of this classifier selection method was found to be considerably better than methods employed hitherto. This confirms the complex nature of the PPI prediction problem and also the necessity of using biological information for classifier fusion. The LocFuse is available at: http://lbb.ut.ac.ir/Download/LBBsoft/LocFuse. The results revealed that if we divide proteome space according to the cellular localization of proteins, then the utility of some classifiers in PPI prediction can be improved. Therefore, to predict the interaction for any given protein pair, we can select the most accurate classifier with regard to the cellular localization information. Based on the results, we can say that the importance of different features for PPI prediction varies between differently localized proteins; however in general, our novel features, which were extracted from position-specific scoring matrices (PSSMs), are the most important ones and the Random Forest (RF) classifier performs best in most cases. LocFuse was developed with a user-friendly graphic interface and it is freely available for Linux, Mac OSX and MS Windows operating systems. •A novel classifier fusion method for human PPI network prediction is proposed.•We exploit eight different genomic/proteomic feature types to encode protein pairs.•New features extracted from PSSMs with high predictive power for PPI prediction.•Dividing proteome space based on cellular localization will improve the prediction.•Proposed method is better than available PPI prediction methods.