If binding sites of a certain TF were frequently found in the off-target set of a candidate site, the binding motif of this TF will be searched as reported in the JASPAR database (http://jaspardev.genereg.net/) [ 23].
This represents the situation in which experimental information concerning the binding patterns of a certain test kinase to the inhibitors is partly available.
In other words, we swap the binding sores of a certain percentage of genes in miR-1 target and non-target gene sets.
Such annotations, however, do not provide quantitative information, like the DNA-binding specificity of a certain TF, because binding-specificities within TF superclasses, and even within TF classes, may vary tremendously.
Accordingly, a polymorphism at the DNA-binding domain of a certain TF can affect the TF's ability to recognize and bind its recognition sites, causing altered expression of all genes regulated by this TF.
When SRSF2 binding exceeds a certain level, inclusion of the alternative exons is ensured.
There is also no over- or underregistration of binding events on a certain RyR within each set of simulations.
As discussed in the Conclusions, we plan to adapt the method to deal with weighted interactions, e.g., the score of a predicted binding or the confidence of a certain experimental technique.
The expression data provides us the chance to evaluate the effect of miRNA binding in the sense of a certain environmental condition and tissue, on the basis of several evidences showing that the expression profiles of miRNAs are closely related to that of their target genes.
