a beta-mixture model for dimensionality reduction, sample classification and analysisbeta-mixture模型降维、样本分类和分析.pdfVIP

Laurila et al. BMC Bioinformatics 2011, 12:215 /1471-2105/12/215 RESEARCH ARTICLE Open Access A Beta-mixture model for dimensionality reduction, sample classification and analysis 1,2 3 3 2,3 3 1 Kirsti Laurila , Bodil Oster , Claus L Andersen , Philippe Lamy , Torben Orntoft , Olli Yli-Harja and Carsten Wiuf2* Abstract Background: Patterns of genome-wide methylation vary between tissue types. For example, cancer tissue shows markedly different patterns from those of normal tissue. In this paper we propose a beta-mixture model to describe genome-wide methylation patterns based on probe data from methylation microarrays. The model takes dependencies between neighbour probe pairs into account and assumes three broad categories of methylation, low, medium and high. The model is described by 37 parameters, which reduces the dimensionality of a typical methylation microarray significantly. We used methylation microarray data from 42 colon cancer samples to assess the model. Results: Based on data from colon cancer samples we show that our model captures genome-wide characteristics of methylation patterns. We estimate the parameters of the model and show that they vary between different tissue types. Further, for each methylation probe the posterior probability of a methylation state (low, medium or high) is calculated and the probability that the state is correctly predicted is assessed. We demonstrate that the model can be applied to classify cancer tissue types accurately and that the model provides accessible and easily interpretable data summaries. Conclusions: We have developed a beta-mixture model for methylation microarray data. The model substantially reduces the dimensionality of the d