title: Explore the hidden treasure in protein-protein interaction networks - an iterative model for predicting protein functions.
abstract: Protein-protein interaction networks constructed by high throughput technologies provide opportunities for predicting protein functions. A lot of approaches and algorithms have been applied on PPI networks to predict functions of unannotated proteins over recent decades. However, most of existing algorithms and approaches do not consider unannotated proteins and their corresponding interactions in the prediction process. On the other hand, algorithms which make use of unannotated proteins have limited prediction performance. Moreover, current algorithms are usually one-off predictions. In this paper, we propose an iterative approach that utilizes unannotated proteins and their interactions in prediction. We conducted experiments to evaluate the performance and robustness of the proposed iterative approach. The iterative approach maximally improved the prediction performance by 50%-80% when there was a high proportion of unannotated neighborhood protein in the network. The iterative approach also showed robustness in various types of protein interaction network. Importantly, our iterative approach initially proposes an idea that iteratively incorporates the interaction information of unannotated proteins into the protein function prediction and can be applied on existing prediction algorithms to improve prediction performance.
authors.affiliation: School of Information Technology, Deakin University, 221 Burwood Highway Burwood, Victoria 3125, Australia.
authors.forename: Derui
authors.initials: D
authors.lastname: Wang
authors.affiliation: School of Information Technology, Deakin University, 221 Burwood Highway Burwood, Victoria 3125, Australia.
authors.forename: Jingyu
authors.initials: J
authors.lastname: Hou
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein / Q000706:statistics & numerical data; D006801:Humans; D008954:Models, Biological; D058977:Molecular Sequence Annotation; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins
keywords: PPI network; algorithm; iterative model; protein function prediction