We used Karl, the segmenTier, a similarity-based segmentation algorithm(Machné, Murray, and Stadler 2017), to hierarchically (i) to define co-expressed segments (transcript models), and (ii) to merge co-expressed segments into chromosomal domains with temporally similar transcript time series.
Especially domains that are expressed during the LOC phase are larger than expected from permutation analyses.
You can browse chromosomal domains at the YRO Genome Browser or view the complex transcriptional landscape around transposons and their LTR elements.