LUX genomic regulation using PBMs and EMA

The promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used for assigning an dissociation constant (Kd). This was performed by inverting Ka=1/Kd and adding up for the full promoter the affinity contribution of each 8-mere. The resulting total Ka was then inverted once more to derive a total dissociation constant, which we report in Supplementary table X. The z-scores for each promoter were calculated by concatenating the genome and sampling randomly regions of the same size of the promoter 10,000. Total dissociation constants for each of the sample regions as was done for their cognate promoter region. The values were ln-transformed and the z-score calculated accordingly with (x-mu)/sigma.