title: Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study.
abstract: Protein-protein interactions in Escherichia coli (E. coli) has been studied extensively using high throughput methods such as tandem affinity purification followed by mass spectrometry and yeast two-hybrid method. This can in turn be used to understand the mechanisms of bacterial cellular processes. However, experimental characterization of such huge amount of interactions data is not available for other important enteropathogens. Here, we propose a support vector machine (SVM)-based prediction model using the known PPIs data of E. coli that can be used to predict PPIs in other enteropathogens, such as Vibrio cholerae, Salmonella Typhi, Shigella flexneri and Yersinia entrocolitica. Different features such as domain-domain association (DDA), network topology, and sequence information were used in developing the SVM model. The proposed model using DDA, degree and amino acid composition features has achieved an accuracy of 82% and 62% on 5-fold cross validation and blind E. coli datasets, respectively. The predicted interactions were validated by Gene Ontology (GO) semantic similarity measure and String PPIs database (experimental PPIs only). Finally, we have developed a user-friendly webserver named EnPPIpred to predict intra-species PPIs in enteropathogens, which will be of great help for the experimental biologists. The webserver EnPPIpred is freely available at http://bicresources.jcbose.ac.in/ssaha4/EnPPIpred/.
authors.affiliation: Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India.
authors.forename: Ranjan Kumar
authors.initials: RK
authors.lastname: Barman
authors.affiliation: Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India.
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Jana
authors.affiliation: Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India.|Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India.
authors.forename: Santasabuj
authors.initials: S
authors.lastname: Das
authors.affiliation: Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India.
authors.forename: Sudipto
authors.initials: S
authors.lastname: Saha
mesh_terms: D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D020407:Internet; D025941:Protein Interaction Mapping; D012372:ROC Curve; D015203:Reproducibility of Results; D012485:Salmonella typhi / Q000378:metabolism; D013045:Species Specificity; D060388:Support Vector Machine; D049490:Systems Biology / Q000379:methods*
chemical_list: D029968:Escherichia coli Proteins