The state of a normal or diseased cell is determined by external signals and by its intrinsic gene expression pat- tern. Transcription factors (TFs) are major regulators of gene expression, typically controlling more than one gene and acting in concert. Such TF-gene interactions can be described as networks, which are crucial to understand hierarchies of gene expression regulation. The identifica- tion of TF binding sites (TFBSs) in genomic DNA sequences has played an important role in predicting tran- scriptional networks. A large number of TFs binds to spe- cific DNA sequence stretches with a length of 5–25 bp (1), which have been experimentally determined and have served to define motifs that are.
