{"title":"贝叶斯混合模型分析检测差异表达基因。","authors":"Zhenyu Jia, Shizhong Xu","doi":"10.1155/2008/892927","DOIUrl":null,"url":null,"abstract":"<p><p>Control-treatment design is widely used in microarray gene expression experiments. The purpose of such a design is to detect genes that express differentially between the control and the treatment. Many statistical procedures have been developed to detect differentially expressed genes, but all have pros and cons and room is still open for improvement. In this study, we propose a Bayesian mixture model approach to classifying genes into one of three clusters, corresponding to clusters of downregulated, neutral, and upregulated genes, respectively. The Bayesian method is implemented via the Markov chain Monte Carlo (MCMC) algorithm. The cluster means of down- and upregulated genes are sampled from truncated normal distributions whereas the cluster mean of the neutral genes is set to zero. Using simulated data as well as data from a real microarray experiment, we demonstrate that the new method outperforms all methods commonly used in differential expression analysis.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2008/892927","citationCount":"5","resultStr":"{\"title\":\"Bayesian mixture model analysis for detecting differentially expressed genes.\",\"authors\":\"Zhenyu Jia, Shizhong Xu\",\"doi\":\"10.1155/2008/892927\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Control-treatment design is widely used in microarray gene expression experiments. The purpose of such a design is to detect genes that express differentially between the control and the treatment. Many statistical procedures have been developed to detect differentially expressed genes, but all have pros and cons and room is still open for improvement. In this study, we propose a Bayesian mixture model approach to classifying genes into one of three clusters, corresponding to clusters of downregulated, neutral, and upregulated genes, respectively. The Bayesian method is implemented via the Markov chain Monte Carlo (MCMC) algorithm. The cluster means of down- and upregulated genes are sampled from truncated normal distributions whereas the cluster mean of the neutral genes is set to zero. Using simulated data as well as data from a real microarray experiment, we demonstrate that the new method outperforms all methods commonly used in differential expression analysis.</p>\",\"PeriodicalId\":73471,\"journal\":{\"name\":\"International journal of plant genomics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2008-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1155/2008/892927\",\"citationCount\":\"5\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International journal of plant genomics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1155/2008/892927\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International journal of plant genomics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1155/2008/892927","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Bayesian mixture model analysis for detecting differentially expressed genes.
Control-treatment design is widely used in microarray gene expression experiments. The purpose of such a design is to detect genes that express differentially between the control and the treatment. Many statistical procedures have been developed to detect differentially expressed genes, but all have pros and cons and room is still open for improvement. In this study, we propose a Bayesian mixture model approach to classifying genes into one of three clusters, corresponding to clusters of downregulated, neutral, and upregulated genes, respectively. The Bayesian method is implemented via the Markov chain Monte Carlo (MCMC) algorithm. The cluster means of down- and upregulated genes are sampled from truncated normal distributions whereas the cluster mean of the neutral genes is set to zero. Using simulated data as well as data from a real microarray experiment, we demonstrate that the new method outperforms all methods commonly used in differential expression analysis.