Figure 1

Visualization methods for illustrating the positional preferences of motif pairs with respect to TSSs. Regions [-2000, +1000] relative to TSSs are regarded as 'promoters' (TSS positions are indicated by arrows in the Class 1 examples; for an explanation of the different classes, see the main text). A motif pair, that of CAAT_01 and E2F_Q6, is shown as an example of the Class 1 motif pairs, while a second pair, that of AFP1 and CEBPgamma, is used as an example of Class 2 pairs. (A) Heat map showing the frequency of the motif pair. Each region, which represents a region-pair, is colored according to the raw counts of the motif pair considered. High counts are shown in red, intermediate counts in white, and low counts in blue. The presence of CAAT_01 (upper figure) and AFP1 (lower figure) are shown on the X-axes for the two examples. (B) Heat map showing the negative logarithm of p-values calculated for the significance of positional preference. (C) Positional distribution of a single motif on promoters. The Y-axis indicates the frequency of the motif at each position represented in the X-axis in all promoters.