Augmented transitive relationships with high impact protein distillation in protein interaction prediction

作者：Tang Yi Tsung; Kao Hung Yu^*

来源：Biochimica et Biophysica Acta-Proteins and Proteomics, 2012, 1824(12): 1468-1475.

DOI：10.1016/j.bbapap.2012.05.013

• Protein-protein interaction
• Transitive relationship

Predicting new protein-protein interactions is important for discovering novel functions of various biological pathways. Predicting these interactions is a crucial and challenging task Moreover, discovering new protein-protein interactions through biological experiments is still difficult. Therefore, it is increasingly important to discover new protein interactions. Many studies have predicted protein-protein interactions, using biological features such as Gene Ontology (GO) functional annotations and structural domains of two proteins. In this paper, we propose an augmented transitive relationships predictor (ATRP), a new method of predicting potential protein interactions using transitive relationships and annotations of protein interactions. In addition, a distillation of virtual direct protein-protein interactions is proposed to deal with unbalanced distribution of different types of interactions in the existing protein-protein interaction databases. Our results demonstrate that ATRP can effectively predict protein-protein interactions. ATRP achieves an 81% precision, a 74% recall and a 77% F-measure in average rate in the prediction of direct protein-protein interactions. Using the generated benchmark datasets from KUPS to evaluate of all types of the protein-protein interaction. ATRP achieved a 93% precision, a 49% recall and a 64% F-measure in average rate. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.

• 出版日期2012-12