a bayesian mixed regression based prediction of quantitative traits from molecular marker and gene expression data基于贝叶斯混合回归预测的定量特征的分子标记和基因表达数据.pdfVIP

A Bayesian Mixed Regression Based Prediction of Quantitative Traits from Molecular Marker and Gene Expression Data 1 ¨ ¨ 2,3,4,5 Madhuchhanda Bhattacharjee *, Mikko J. Sillanpaa 1 Department of Statistics, University of Pune, Pune, Maharashtra, India, 2 Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, 3 Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland, 4 Department of Mathematical Sciences, University of Oulu, Oulu, Finland, 5 Department of Biology, University of Oulu, Oulu, Finland Abstract Both molecular marker and gene expression data were considered alone as well as jointly to serve as additive predictors for two pathogen-activity-phenotypes in real recombinant inbred lines of soybean. For unobserved phenotype prediction, we used a Bayesian hierarchical regression modeling, where the number of possible predictors in the model was controlled by different selection strategies tested. Our initial findings were submitted for DREAM5 (the 5th Dialogue on Reverse Engineering Assessment and Methods challenge) and were judged to be the best in sub-challenge B3 wherein both functional genomic and genetic data were used to predict the phenotypes. In this work we further improve upon this previous work by considering various predictor selection strategies and cross-validation was used to measure accuracy of in- data and out-data predictions. The results from various model choices indicate that for this data use of both data types (namely functional genomic and genetic) simultaneously improves out-data prediction accuracy. Adequate goodness-of-fit can be easily achieved with more complex models for both phenotypes, since the number of potential predictors is large