Figure 1.
The algorithm to detect the positional association of motifs in close vicinity. The frequency tables are converted into PWM, and the cutoff is determined as described in the text. Each PWM with the corresponding threshold for OFr = 0.0001 is mapped in both the promoter sequences and shuffled sequences. After comparing the number of occurrences in both the data sets, TFs having significantly higher occurrence in the promoter sequences are selected with the criteria z-score >3. Further, to find out the positional associations of the TFs with respect to MyoD, each observed occurrence distribution is compared with the background distribution, and positions having z-score >10 are selected as preferred positions.