a bayesian model for classifying all differentially expressed proteins simultaneously in 2d page gels分类的贝叶斯模型同时在2 d页面所有差异表达蛋白质凝胶.pdfVIP

Wu et al. BMC Bioinformatics 2012, 13:137 /1471-2105/13/137 METHODOLOGY ARTICLE Open Access A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels 1,2,5* 3 4 1,2,6 Steven H Wu , Michael A Black , Robyn A North and Allen G Rodrigo Abstract Background: Two-dimensional polyacrylamide gel electrophoresis (2D PAGE) is commonly used to identify differentially expressed proteins under two or more experimental or observational conditions. Wu et al (2009) developed a univariate probabilistic model which was used to identify differential expression between Case and Control groups, by applying a Likelihood Ratio Test (LRT) to each protein on a 2D PAGE. In contrast to commonly used statistical approaches, this model takes into account the two possible causes of missing values in 2D PAGE: either (1) the non-expression of a protein; or (2) a level of expression that falls below the limit of detection. Results: We develop a global Bayesian model which extends the previously described model. Unlike the univariate approach, the model reported here is able treat all differentially expressed proteins simultaneously. Whereas each protein is modelled by the univariate likelihood function previously described, several global distributions are used to model the underlying relationship between the parameters associated with individual proteins. These global distributions are able to combine information from each protein to give more accurate estimates of the true parameters. In our implementation of the procedure, all parameters are recovered by Markov chain Monte Carlo (MCMC) integration. The 95% highest posterior density (HPD) intervals for the marginal posterior distributions are used to d