Time course gene expression experiments

Gene expression profiles, resulting from time course experiments, must include relevant statistical information, and also be easy to visualize, group, and analyze to give biologically relevant insights. Here we present and demonstrate a method to obtain and analyze sets of genome-wide “standardized expression profiles” (SEPs). SEPs can be estimated from RNA-Seq or microarray experiments that sample the transcriptome at different times, using a minimum of two biological replicates per time point. We begin by discussing the design of such experiments, and then exemplify the advantages of SEPs by applying the method to the study of the changes in the transcriptomes of chili pepper (Capsicum annuum L.) fruits during development. The method, which is applicable to any replicated time course experiment, is presented here for the R platform, and data as well as functions for SEP analyses in the chili pepper experiment are publicly available as an R package. SEPs can also be employed as the starting point for gene expression network estimation.