Ranks of known TAL effector target sites.

<p>Ranks of known TAL effector target sites among the TALgetter predictions in independent cross validation-like experiments (TALgetter CV) and for the final version used in the web-application and command line program (TALgetter final).</p

Positional preference of TAL effector target sites relative to the TATA-box (left) and TC-box (right).

<p>The estimated density of positions from the positive set is plotted as a green line, while the density of the negatives is plotted in red. The green points at the bottom of the plots represent the distribution of positions from the positive set along the x-axis, where the points are distributed randomly in y-direction to make individual points distinguishable.</p

Visualization of the parameters of TALgetter.

<p>(A) The nucleotide preferences for position 0 are visualized as a sequence logo. (B) The binding specificities for the different RVDs are plotted in analogy to sequence logos as well, whereas the probabilities representing importance of RVDs are plotted against the RVDs as blue points connected by a black line. (C) Total weight of each RVD in the training data set.</p

Positional preference of TAL effector target sites relative to the start codon (left) and the transcription start site (TSS, right).

<p>The estimated density of positions from the positive set is plotted as a green line, while the density of the negatives is plotted in red. The whiskers indicate the bandwith of the box kernel used to smooth the curves in a kernel density estimation. The green points at the bottom of the plots represent the distribution of positions from the positive set along the x-axis, where the points are distributed randomly in y-direction to make individual points distinguishable.</p

Predicted targets in <i>C. sinensis</i> (2).

<p>List of predicted targets in <i>C. sinensis</i>. For each predicted target, we list the name of the TAL effector, the distance from the 3′ end of the target site to the start codon, and the sequence of the target site.</p

Additional file 1 of DiffLogo: a comparative visualization of sequence motifs

Supplementary Methods, Results, Figures, and Examples. This file is structured in four sections. Section 1, Additional examples, contains Figures S1 and S2. Figure S1 shows a DiffLogo grid for nine CTCF motifs. Figure S2 shows a DiffLogo grid for four F-box domain motifs. In section 2, CTCF with and without clustering, we show in detail the impact of clustering and optimal leaf ordering for a DiffLogo grid of nine CTCF motifs. In section 3, Alternative combinations of stack heights and symbol weights, we first describe the mathematical background of four implementations of H ℓ and two implementations of r ℓ,a . Afterwards, we show the result of the eight possible combinations in Tables S1 and S2 on two sequence motifs. In section 4, Tool comparison, we compare DiffLogo with the five tools seqLogo, iceLogo, MotifStack, STAMP, and Two Sample Logo. From the set of nine CTCF motifs we selected the pair of motifs with the highest similarity according to the Jensen-Shannon divergence (GM12878 and K562) and the pair of motifs with the lowest similarity according to the Jensen-Shannon divergence (H1-hESC and HUVEC) for the comparison of the five different tools. (PDF 8775 kb

Predicted targets in <i>O. sativa</i>.

<p>List of predicted targets in <i>O. sativa</i>. For each predicted target, we list the name of the TAL effector, the locus ID and the description of the targeted gene, the rank among the predictions of TALgetter for the specific TAL effector, and the list of microarray experiments that support this target. The corresponding log-fold changes observed in the microarray experiments are given in parentheses. TAL effectors with a common target site are listed in the same row. If both TAL effectors have identical RVD sequences, they are separated by a slash. Otherwise, they are separated by an ampersand. Known target sites are marked with an asterisk.</p

Comparison of TALgetter to Target Finder on the gene expression data from transgenic <i>A. thaliana</i> lines.

<p>We consider as performance measures the number of predicted targets consistent with up-regulation in gene expression microarrays for different rank cutoffs and thresholds of 1 and 0.5 on the log-fold changes (left panel), and the precision-recall (PR) curve (right panel) using a threshold of 1 on the log-fold changes.</p

Summary of the evaluations presented in Figure 1.

<p>For each rank cutoff (10, 20, 50, 100), we count the number of data sets where a prediction program outperforms the other (bars colored identical to program), or both score equally well (bars colored gray).</p

Venn diagrams of the predictions of the three programs using a log fold-change of 1 and a rank cutoff of 100.

<p>Venn diagrams of the predictions of the three programs using a log fold-change of 1 and a rank cutoff of 100.</p