The visualization of the gene-level effects of 5'-TTAAAA intron motif density on intron Alu density obtained from the proposed two step regression method. The data points are labeled with chromosome IDs. The X- and Y- coordinates are the negatives of the log10 transformed p-values (adjusted with BH method) from the two models, respectively. The dashed red lines correspond to 0.05 in the scale of adjusted p-values. Model-1 evaluates the effect of the motif density on the presence or absence of Alus in the introns of the genes. Model-2 evaluates the effect of the motif density on the intron Alu density of the genes with at least one Alu repeat in their intron regions. All the regression coefficients β are positive in the model-1 and the coefficients β* are positive in model-2 except for chromosomes 7 and X (marked with blue).
Zhang et al. BMC Genomics 2011 12:157 doi:10.1186/1471-2164-12-157