bayesian markov random field analysis for protein function prediction based on network data贝叶斯马尔可夫随机场分析蛋白质功能预测基于网络数据.pdfVIP

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data 1 2 1 2,3 Yiannis A. I. Kourmpetis , Aalt D. J. van Dijk , Marco C. A. M. Bink , Roeland C. H. J. van Ham , Cajo J. F. ter Braak1* 1 Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands, 2 Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands, 3 Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands Abstract Inference of protein functions is one of the most important aims of modern biology. To fully exploit the large volumes of genomic data typically produced in modern-day genomic experiments, automated computational methods for protein function prediction are urgently needed. Established methods use sequence or structure similarity to infer functions but those types of data do not suffice to determine the biological context in which proteins act. Current high-throughput biological experiments produce large amounts of data on the interactions between proteins. Such data can be used to infer interaction networks and to predict the biological process that the protein is involved in. Here, we develop a probabilistic approach for protein function prediction using network data, such as protein-protein interaction measurements. We take a Bayesian approach to an existing Markov Random Field method by performing simultaneous estimation of the model parameters and prediction of protein functions. We use an adaptive Markov Chain Monte Carlo algorithm that leads to more accurate parameter estimates and consequently to improved prediction performance compared to the standard Markov R