MvGST: Multivariate and Directional Gene Set Testing

• Activity Number: 353
• Type: Contributed
• Date/Time: Tuesday, August 11, 2015 : 10:30 AM to 12:20 PM
• Sponsor: Section on Statistics in Genomics and Genetics
• Author(s): John Stevens* and Dennis Mecham and Garrett Saunders and S. Clay Isom
• Companies: Utah State University and Utah State University and Brigham Young University - Idaho and Utah State University
• Keywords: RNA-Seq ; microarray ; multiple comparisons ; gene set testing

Abstract

Gene expression research often seeks to characterize differentially expressed genes based on their role in sets such as GO terms. Previous gene set testing methods have focused on experimental designs where there is a single null hypothesis for each gene. However, commonly-used designs naturally lead to multiple null hypotheses for each gene (such as at multiple time points), and the characterization of these multivariately differentially expressed genes is of great interest. The R package mvGST provides platform-independent tools to identify GO terms that are differentially active (up or down) in comparisons (contrasts) of interest. Where multiple contrasts are of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile, with adjustments for multiple testing within the structure of the GO graph.