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. 2011 Sep 9;6(9):e24279. doi: 10.1371/journal.pone.0024279

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Erb, van Nimwegen.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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The horizontal axes in panels A, B, and D show the location relative to TSS, where upstream positions are denoted by negative numbers. A: The vertical axis shows the total number of sites as a function of position summed over all 79 WMs and all promoter regions, with the solid line showing a smoothed version of the raw distribution (dots). B: TFBS distributions for several example TFs. The vertical axis shows smoothed frequency of site occurrence as a function of position for the TFs SPT15 (TATA binding protein), GAT1, SUM1, MCM1, CBF1, and REB1. C: Cumulative distribution of the position of highest TFBS density. Each dot corresponds to one motif. Only the motifs with a sufficient number of predicted TFBSs were used, see Methods. D: TFBS distributions relative to TSS for the proximal promoter motifs ROX1 (gray), FKH1 (dark blue), SPT15 (red), GAT1 (green), PBF1/2 (pink), RPN4 (light blue), and NDT80 (black). The inset shows a suggested alignment of the corresponding motifs.

Inline graphic — The horizontal axes in panels A, B, and D show the location relative to TSS, where upstream positions are denoted by negative numbers. A: The vertical axis shows the total number of sites as a function of position summed over all 79 WMs and all promoter regions, with the solid line showing a smoothed version of the raw distribution (dots). B: TFBS distributions for several example TFs. The vertical axis shows smoothed frequency of site occurrence as a function of position for the TFs SPT15 (TATA binding protein), GAT1, SUM1, MCM1, CBF1, and REB1. C: Cumulative distribution of the position of highest TFBS density. Each dot corresponds to one motif. Only the motifs with a sufficient number of predicted TFBSs were used, see Methods. D: TFBS distributions relative to TSS for the proximal promoter motifs ROX1 (gray), FKH1 (dark blue), SPT15 (red), GAT1 (green), PBF1/2 (pink), RPN4 (light blue), and NDT80 (black). The inset shows a suggested alignment of the corresponding motifs.