Figure 3.

Regions of low gene density contain significantly more genes of high regulatory complexity. (a) Window size (in base pairs) of an 11-gene sliding window across the X chromosome versus position along the chromosome. The horizontal line at 250,000 bp indicates the cutoff above which a window was designated as low density. A total of 53 windows larger than 250,000 bp were identified on the X chromosome. These windows overlap to generate 14 independent peaks, numbered 1 through 14. Normalized FBx and BDGPx scores for each gene were calculated by dividing the raw index score by the maximum score for that index. The normalized scores of all low-density windows were compared to the scores of all 11-gene windows on the chromosome. The expression complexity score for low gene density windows was significantly greater than the average score for all possible windows on the X chromosome (Welch ANOVA, p < 0.008; Wilcoxon two-sample test, p < 0.03). (b) The 11 genes flanking the highest point of each numbered peak on the X chromosome. Genes boxed in red fall in the top 20% of expression complexity by FBx or the top 24% by BDGPx. Genes in unshaded boxes have expression data available, but do not fall in the upper range of the FBx or BDGP indices. Genes that are shaded, which represent the majority of genes in these windows, have no expression data available. This panel indicates only genes in the highest central peak. However, all genes within windows exceeding 250,000 bp in size were used for the statistical analysis described above.

Nelson et al. Genome Biology 2004 5:R25  
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