scholarly journals A Generalized Mixture Model for Detecting Differentially Expressed Genes in Microarray Experiments

2016 ◽  
Vol 1 (4) ◽  
Author(s):  
Mehdi Razzaghi ◽  
◽  
Dong Zhang ◽  
Keyword(s):  
Mixture Model ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Microarray Experiments

scholarly journals Bayesian Mixture Model Analysis for Detecting Differentially Expressed Genes

2008 ◽  
Vol 2008 ◽  
pp. 1-12 ◽  
Author(s):  
Zhenyu Jia ◽  
Shizhong Xu
Keyword(s):  
Mixture Model ◽  
Differentially Expressed Genes ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
Control Treatment ◽  
Microarray Gene Expression ◽  
Bayesian Mixture Model ◽  
Bayesian Mixture ◽  
Truncated Normal ◽  
Upregulated 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.

scholarly journals A New Test Statistic Based on Shrunken Sample Variance for Identifying Differentially Expressed Genes in Small Microarray Experiments

2008 ◽  
Vol 2 ◽  
pp. BBI.S473 ◽  
Author(s):  
Akihiro Hirakawa ◽  
Yasunori Sato ◽  
Chikuma Hamada ◽  
Isao Yoshimura
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Simulation Studies ◽  
Test Statistic ◽  
Microarray Experiments ◽  
Cancer Data ◽  
False Discovery ◽  
The Mean ◽  
Sample Variances ◽  
Better Than

Choosing an appropriate statistic and precisely evaluating the false discovery rate (FDR) are both essential for devising an effective method for identifying differentially expressed genes in microarray data. The t-type score proposed by Pan et al. (2003) succeeded in suppressing false positives by controlling the underestimation of variance but left the overestimation uncontrolled. For controlling the overestimation, we devised a new test statistic (variance stabilized t-type score) by placing shrunken sample variances of the James-Stein type in the denominator of the t-type score. Since the relative superiority of the mean and median FDRs was unclear in the widely adopted Significance Analysis of Microarrays (SAM), we conducted simulation studies to examine the performance of the variance stabilized t-type score and the characteristics of the two FDRs. The variance stabilized t-type score was generally better than or at least as good as the t-type score, irrespective of the sample size and proportion of differentially expressed genes. In terms of accuracy, the median FDR was superior to the mean FDR when the proportion of differentially expressed genes was large. The variance stabilized t-type score with the median FDR was applied to actual colorectal cancer data and yielded a reasonable result.

Grouping Rank Product Meta-Analysis Method for Identifying Differentially Expressed Genes in Microarray Experiments

2010 ◽  
Vol 44-47 ◽  
pp. 905-909
Author(s):  
Yuan Tian ◽  
Gui Xia Liu ◽  
Chun Guang Zhou
Keyword(s):  
Differentially Expressed Genes ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Analysis Approach ◽  
Analysis Method ◽  
Experimental Conditions ◽  
Microarray Experiments ◽  
Rank Product ◽  
Product Approach ◽  
Improved Model

One of the main purposes in analysis of microarray experiments is to identify differentially expressed genes under two experimental conditions. The Meta-analysis method, rank product meta-analysis approach, considered a powerful tool for identification of differentially expressed genes. However, rank product meta-analysis approach used the each dataset in the computation of the fold changes, which leaded to less computational efficiency. Here we modified the rank product meta-analysis approach to obtain an improved model for identifying different gene expression. The new model, grouping rank product approach, adds competitive classification of samples to group datasets before the computation of the fold changes. We used the grouping rank product approach on two simulated datasets and two breast datasets and showed that the grouping rank product approach is not only as accurate as the rank product meta-analysis approach, but also more computational efficient in identifying differentially expressed genes.

scholarly journals Statistical tests for identifying differentially expressed genes in time-course microarray experiments

2003 ◽  
Vol 19 (6) ◽  
pp. 694-703 ◽  
Author(s):  
T. Park ◽  
S.-G. Yi ◽  
S. Lee ◽  
S. Y. Lee ◽  
D.-H. Yoo ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Time Course ◽  
Statistical Tests ◽  
Differentially Expressed ◽  
Microarray Experiments
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