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Asian Journal of Animal and Veterinary Advances

Year: 2012 | Volume: 7 | Issue: 8 | Page No.: 745-753
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Authors

W.Y. Liu

C.J. Zhao

Keywords

Short Communication

Simulation Analysis of the Selection of Differential Expression Genes Correlated with Phenotype Data in Chicken Microarray Experiments

W.Y. Liu and C.J. Zhao
DNA microarrays can measure the differential expression of hundreds and thousands of genes to identify changes in their expression between pair-wise biological states. Although, many methods are developed to determine the significance of these changes while accounting for the enormous number of genes, there is no uniform or standard method for different microarray experiments to date. Researches are often confused with diverse algorithm issues, especially the changing fold of differential expression genes, in the selection of suitable candidate genes. Here, a simulation was described to analyze the microarray experimental data correlated with corresponding biological phenotypes, aiming at to measure the proper fold changes of differential expression genes with rigorous statistics of p values and acceptable FDRs (false discovery rates) in permutated univariate tests. The result showed that the commonly used fold change method of candidate gene selection was relatively reasonable and the variation scope was suggested as fold changes of 1.5-2.1. The fold changes no less than 1.5 of gene expression would be a good choice of gene selection with stable gene numbers passed the filtering criteria. When the data filtering fold change was rigid, the number of genes passed the filtering criteria turned to decrease sharply. The present analysis provided a good basis for further gene expression studies.
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