title: Predicting protein-protein interactions between human and hepatitis C virus via an ensemble learning method.
abstract: An estimated 170 million people, approximately 3% of the world population, are chronically infected with the hepatitis C virus (HCV). More than 350,000 deaths are reported annually, which are caused by HCV. HCV, similar to a variety of viruses, causes disease in humans by altering protein-protein interactions within the host cells. Experimental approaches for the detection of host-virus PPIs have many inherent limitations. Computational approaches to predict these interactions are therefore of significant importance. While many studies have been developed to predict intra-species PPIs in the last decade, predictions on inter-species PPIs such as human-HCV PPIs are rare. In this study, we developed an ensemble learning method to predict PPIs between human and HCV proteins. Our model utilises four well-established diverse learners as base classifiers including random forest (RF), Naïve Bayes (NB), support vector machine (SVM) and multilayer perceptron (MLP). In addition, an MLP was used as a meta-learner to combine base learners' predictions to provide the final prediction. To encode human and HCV proteins as feature vectors, we used six different descriptors as follows: amino acid composition (ACC), pseudo amino acid composition (PAC), evolutionary information feature, network centrality measures, tissue information and post-translational modification information. To assess the prediction power of the proposed method, we assembled a benchmark dataset composed of confident positive and negative PPIs. In a 10-fold cross-validation experiment, our prediction method achieved accuracy and specificity as high as 83% and 94%, respectively. Furthermore, in an independent test set the proposed method achieved an accuracy of 84% and a specificity of 92%. When compared with the existing method, our method showed a better performance. These results revealed that our method is suitable for performing PPI prediction in a host-pathogen context.
authors.affiliation: Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
authors.forename: Abbasali
authors.initials: A
authors.lastname: Emamjomeh
authors.forename: Bahram
authors.initials: B
authors.lastname: Goliaei
authors.forename: Javad
authors.initials: J
authors.lastname: Zahiri
authors.forename: Reza
authors.initials: R
authors.lastname: Ebrahimpour
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D016174:Hepacivirus / Q000737:chemistry*; D054884:Host-Pathogen Interactions; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D060388:Support Vector Machine; D014764:Viral Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins; D014764:Viral Proteins