Acute long-day genes

Acute long-day genes are ones whose expression patterns were changed on the first long-day after the transition from the short-day to the long-day condition.

Method to identify acute long-day genes

To identify acute long-day genes, we sought to retrieve probe sets whose expression patterns in the short-day condition and advance condition were significantly different but whose expression patterns in the short-day condition and delay condition were not significantly different. First, we estimated that the phase delay of the advance condition and the delay condition against the short-day condition was approximately 0 hours (~0.88 hours), and 4 hours (~3.96 hours), respectively, using the method described in the above circadian-time analysis from the time-course expression data. In order to complement these phase differences, we set the short-day ZT0 to correspond with the advance condition ZT0, and the short-day ZT20 with the delay condition ZT0. We then performed the same statistical procedures described above for identifying genes whose time-course expression patterns in the short-day and long-day condition were different. In this case, we chose genes whose expressions were significantly different between the short-day condition and the advance condition, but were not significant between the short-day condition and the delay condition.