Frequency distributions of TFBS may have different patterns around the start of transcription (position 0 on the horizontal axis).

<p>X-axis shows the distance from TSS, Y-axis reflects the frequency of motif in each window. Frequencies of ARALY493022_04 TFBS (Class 1) are plotted on the left panel, of RAP26_03 TFBS (Class 2) on the middle panel, and of MYB111_02 (Class 3) on the right panel.</p

Suppression of site loss caused by nucleotide variants in promoters.

<p>Suppression of site loss caused by nucleotide variants in promoters.</p

Features of the nucleotide consensus around TSS.

<p>A top left) Frequency of CA, B top right) Frequency of TATA motif, D middle feft) Frequencies of nucleotides A, C, G, T around TSS for Fgenesh, E middle right) Frequencies of A, C, G, T around TSS for MSU, F bottom) CG skew (), calculated in the window of 40 nt.</p

Basic CNN architecture that was used in building promoter models implemented in the learnCNN.py program [3, 10].

<p>Basic CNN architecture that was used in building promoter models implemented in the learnCNN.py program [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187243#pone.0187243.ref003" target="_blank">3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187243#pone.0187243.ref010" target="_blank">10</a>].</p

Suppression of site gain caused by nucleotide variation in promoters.

<p>Suppression of site gain caused by nucleotide variation in promoters.</p

Promoter classification accuracy.

<p>Promoter classification accuracy.</p

Assessment of promoter prediction quality in Arabidopsis (left) and corn (right).

<p>Arabidopsis genome shows more pronounced consensus at TSS, with higher frequency of TATA motif at -30 and CA at TSS.</p

Expression specificity of TF from Class 1 and 2.

<p>Expression specificity of TF from Class 1 and 2.</p

Methylation around transcription start site in rice in different sequence contexts.

<p>Red–CG, green—CHG, blue–CHH, where H denotes A, C or T nucleotide.</p

An example of five distinct TFBS entries in the TRANSFAC database with very similar position weight matrices (PWMs).

<p>An example of five distinct TFBS entries in the TRANSFAC database with very similar position weight matrices (PWMs).</p