Fig. 3

Motif orientation preferences as a function of distance from the transcription start site (TSS). Based on mapping statistics alone, the percentage of motifs with significant (binomial test p < 0.05, Benjamini-Hochberg (BH) corrected) to upstream intervals of length 100 nt at different distances from the transcription start site (TSS). Statics were generated for the set of actual motifs (black line) as well as randomized motifs based on the composition of the respective interval (blue line) or based on motif-base compositions (magenta line). For randomized motifs, 10 repeats were performed and the average percentage of motifs with orientation preference computed. P-values indicate significant departure of the respective random expectation from true motifs (binomial test, BH-corrected). Motifs were required to map ten times or more to the respective upstream regional interval or ignored otherwise