Figure 5

Density of TRE consensus Hexamers for various promoter groups. Sequences in promoter groups a-f were scanned for half sites with a PWM [40] score threshold of 6.0. Probability density functions for the number of TRE half sites observed per 1000 bps are shown for each class of DNA sequence. Estrogen regulated genes (group d) were chosen for this comparison since the characterized motif for their nuclear receptor is highly similar with the exception that the orientation of the motif is a palindrome with a 3 nucleotide spacer. These curves show the density of TRE half sites per 1000 bps for: a. in permutations of random promoter regions (n = 50). b. Randomly selected promoter regions (n = 50). c. promoter region for genes with TH regulated promoter regions (n =28). d. promoter region for genes with estrogen regulated promoter regions (n = 50). e. Regions detected by Splitter (n = 100), and f. validated regions detected by Splitter (n = 36). The results shown by a are random nucleotide permutations of the promoter regions shown in b. On the y-axis, density is the empirical estimate of the underlying probability density function. Regions a-d are 10 kbps in length where regions e,f are in the 300-600 bps range.