The DNA binding specificity of transcription factors (TFs) is typically represented in the form of a position weight matrix (PWM), also known as a DNA motif. A PWM is a matrix that specifies, for each position in the DNA binding site of a TF, the "weight" or contribution of each possible nucleotide. DNA motifs can be derived from various types of TF-DNA binding data, from small collections of known TF binding sites to large data sets generated using high-throughput technologies. One drawback of this simple model of DNA binding specificity is that it makes the implicit assumption that individual base pairs within a TF binding site contribute independently to the TF-DNA binding affinity. Although this assumption does not always hold, PWM models have been shown to provide reasonable approximations to the DNA binding specificity, and they are still widely used in practice. DNA motifs are currently available for more than 150 Saccharomyces cerevisiae TFs. Here, we briefly describe how these models are built, we provide information on databases containing DNA motifs for S. cerevisiae TFs, and we introduce guidelines on how to interpret the motifs and use them in practice to generate hypotheses about transcriptional regulatory regions.
© 2016 Cold Spring Harbor Laboratory Press.