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Figure 2 | BMC Plant Biology

Figure 2

From: Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

Figure 2

Output of the applied randomization algorithm. A) Background motif abundance of the GRE motif. The parameter “number of promoters with a motif” was exemplarily determined for the GRE motif in several randomized promoter datasets (1000 random sets of 304 genes) and its distribution is visualised in the given histogram. Experimental datasets which exhibit a significant enrichment or depletion (for e.g. the GRE motif) should display a respective significant shift in their position in the background distribution. B) Background motif density of the GRE motif. The parameter “motif counts per promoter” was exemplarily determined for the GRE motif in several randomized promoter datasets (1000 random sets of 304 genes) and the average number of motif counts per promoter is visualised in the given histogram. Experimental datasets which exhibit a significant enrichment or depletion should display a respective significant shift in their position in the background distribution. C) Background dataset composition. Illustration of the number of times a promoter was randomly drawn to participate in the reference dataset. The algorithm draws individual promoters from genomic datasets only once or twice (average from 1000 dataset randomizations), indicating that only very limited redundancy is present in the background dataset modelling. D) False-positive error rate estimations for parameter I. The error rates for genomic frequent and infrequent motifs used in this study are given. It was calculated for each motif in differently sized random datasets (50, 200 and 1000). The approach performed well on all dataset sizes, however becomes inaccurate if the background distribution of the motif (e.g. MRE2) is not approximately Gaussian. The given false-positive error frequency is the number of p-value calls (x-axis) under a set α value (y-axis) observed in 1000 random calculation repetitions.

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