Photoperiodic genes

Photoperiodic genes are significantly and highly changed their expressions between short-day and long-day conditions. Short-day genes were expressed higher in short-day condition than in long-day. Long-day genes were expressed higher in long-day condition than in short-day.

Method to identify photoperiodic genes

To identify the photoperiodic genes, we used time-course expression data under chronic short-day and long-day conditions. In order to complement the observed phase difference between short-day and long-day conditions (the approximately 8 hours), we shifted time points by 8 hours; that is, the short-day ZT16, 20, 0, 4, 8, 12 corresponded to long-day ZT0, 4, 8, 12, 16, 20, respectively. We used log-2-transformed expression values of the GeneChip data in the following analysis. We performed a two-way ANOVA to test the difference in expression levels between the short-day and long-day conditions for each probe set, and assigned P-values and FDRs. We selected as significantly differently expressed genes those whose FDRs were less than or equal to 0.05 and for which the difference between the maximum expression value in the short-day condition and the minimum value in the long-day condition (short-day gene) or between the maximum expression in the long-day condition and the minimum in the short-day condition (long-day gene) was more than 2.5-fold.