capturing heterogeneity in gene expression studies by surrogate variable analysis捕捉异质性通过代理变量分析基因表达的研究.pdfVIP

Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis 1 1,2* Jeffrey T. Leek , John D. Storey 1 Department of Biostatistics, University of Washington, Seattle, Washington, United States of America, 2 Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s) of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. We show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. Not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. This phenomenon is true even for well-designed, randomized studies. We introduce ‘‘surrogate variable analysis’’ (SVA) to overcome the problems caused by heterogeneity in expression studies. SVA can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies. Citation: Leek JT, Storey JD (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 3(9): e161. doi:10.1371/journal.pgen.