Using machine learning techniques and genomic/proteomic information from known databases for defining relevant features for PPI classification

Abstract

In modern proteomics, prediction of protein–protein interactions (PPIs) is a key research line, as these interactions take part in most essential biological processes. In this paper, a new approach is proposed to PPI data classification based on the extraction of genomic and proteomic information from well-known databases and the incorporation of semantic measures. This approach is carried out through the application of data mining techniques and provides very accurate models with high levels of sensitivity and specificity in the classification of PPIs. The well-known support vector machine paradigm is used to learn the models, which will also return a new confidence score which may help expert researchers to filter out and validate new external PPIs. One of the most-widely analyzed organisms, yeast, will be studied. We processed a very high-confidence dataset by extracting up to 26 specific features obtained from the chosen databases, half of them calculated using two new similarity measures proposed in this paper. Then, by applying a filter–wrapper algorithm for feature selection, we obtained a final set composed of the eight most relevant features for predicting PPIs, which was validated by a ROC analysis. The prediction capability of the support vector machine model using these eight features was tested through the evaluation of the predictions obtained in a set of external experimental, computational, and literature-collected datasets.