All the examples in this manual are based on the Arabidopsis cell cycle expression data by Menges et al., 2003⁽¹⁾. Two alternative methods (aphidicolin addition and sucrose starvation) have been used to synchronize cells for genome-wide expression profiling in Arabidopsis cell suspensions, one method generating a synchronized resumption of the S-phase, and the second method resulting in a synchronized transition from G1 to S. An efficient synchronization of Arabidopsis cell cultures is still very difficult to achieve and the average duration of synchronization is highly dependent on the particular method used. Menges et al., 2003⁽¹⁾ have succeeded in covering 19 hours or 3/4 cycle with the aphidicolin addition synchronization and only 12 hours or a little bit more than 1/2 cycle with the sucrose starvation synchronization. In this respect, GenTχWarper features are demonstrated on sub-optimal data. Using yeast (Saccharomyces cerevisiae) cell cycle expression data, where one can achieve up to 2.5 cycles synchronization, might be a better choice. However, our motivation is to promote bioinformatics tools, which are not solely used on yeast data, and consequently encourage development of new experimental techniques allowing the production of plant gene expression time series data that is more suitable for computational biology research.

The raw data has been preprocessed with the RMA method in Bioconductor. Consequently, p-values for regulation have been estimated via permutation tests. In the template matching mode a refined subset of 3277 genes with the lowest p-values for regulation has been used.

⁽¹⁾ Menges,M., Henning,L., Gruissem,W., Murray,A.H. Genome-wide gene expression in an Arabidopsis cell suspension. Plant Molecular Biology, 53, 423-442 (2003).