Paper Info
Title
Computational prediction of the human-microbial oral interactome.
Abstract
The oral cavity is a complex ecosystem where human chemical compounds coexist with a particular microbiota. However, shifts in the normal composition of this microbiota may result in the onset of oral ailments, such as periodontitis and dental caries. In addition, it is known that the microbial colonization of the oral cavity is mediated by protein-protein interactions (PPIs) between the host and microorganisms. Nevertheless, this kind of PPIs is still largely undisclosed. To elucidate these interactions, we have created a computational prediction method that allows us to obtain a first model of the Human-Microbial oral interactome.We collected high-quality experimental PPIs from five major human databases. The obtained PPIs were used to create our positive dataset and, indirectly, our negative dataset. The positive and negative datasets were merged and used for training and validation of a naïve Bayes classifier. For the final prediction model, we used an ensemble methodology combining five distinct PPI prediction techniques, namely: literature mining, primary protein sequences, orthologous profiles, biological process similarity, and domain interactions. Performance evaluation of our method revealed an area under the ROC-curve (AUC) value greater than 0.926, supporting our primary hypothesis, as no single set of features reached an AUC greater than 0.877. After subjecting our dataset to the prediction model, the classified result was filtered for very high confidence PPIs (probability ≥ 1-10-7), leading to a set of 46,579 PPIs to be further explored.We believe this dataset holds not only important pathways involved in the onset of infectious oral diseases, but also potential drug-targets and biomarkers. The dataset used for training and validation, the predictions obtained and the network final network are available at http://bioinformatics.ua.pt/software/oralint.
Year
DOI
Venue
2014
10.1186/1752-0509-8-24
BMC systems biology
Keywords
Field
DocType
bioinformatics,computational biology,systems biology,algorithms
Interactome,Biology,Microbial colonization,Systems biology,Cell biology,Periodontitis,Bioinformatics,Oral cavity
Journal
Volume
Issue
ISSN
8
1
1752-0509
Citations 
PageRank 
References 
8
0.52
35
Authors
8
Name
Order
Citations
PageRank
Edgar D. Coelho1152.82
Joel Arrais2298.85
Sérgio Matos341529.51
Carlos Pereira481.20
Nuno Rosa581.54
Maria José Correia681.54
Marlene Barros781.20
José Luis Oliveira876084.03