Figure 2.

The coefficients of the Poisson linear models in different datasets. The coefficients of the Poisson linear model in the eight sub-datasets when we consider surrounding sequences as 40 nucleotides before and 40 nucleotides after the first nucleotide of a read. Position -1, 0, 1 means the nucleotide before the first nucleotide of a read, the first nucleotide of a read, and the second nucleotide of a read, respectively. Color coding for nucleotides: red, T; green, A; blue, C; black, G. The coefficients for nucleotide T (red) are the base levels, so they are always zero. (a) Coefficients in the Wold data. Shape coding for sub-datasets: rectangle, brain; triangle, liver; circle, skeletal muscle. (b) Coefficients in the Burge data. Shape coding for sub-datasets: rectangle, group 1; triangle, group 2; circle, group 3. (c) Coefficients in the Grimmond data. Shape coding for sub-datasets: rectangle, EB; triangle, ES. Following are examples of how these coefficients should be read. In the Wold brain data, the coefficient of C in the first nucleotide of a read (the blue rectangle at position 0 in (a)) is 0.82. This means that if the nucleotide T is replaced by C, then the sequencing preference will increase to e0.82 = 2.27 times. Nt: nucleotides.

Li et al. Genome Biology 2010 11:R50   doi:10.1186/gb-2010-11-5-r50
Download authors' original image