The ChIP data from mapping yeast genome transcriptional network i

The ChIP data from mapping yeast genome transcriptional network indicated information content in nonspecific binding profiles. The occurrence of this may be due to TF-DNA interactions which are functionally organized although they are not indicating any highly specific interactions. Such information content may also be as a result of experimental or normalization artifacts thus nullifying the research highlight of the paper. To strengthen the highlight, ChIP binding ratios were compared to the sequence-based predictions of TF affinities. The predicstion is usually done using the Position Weight Matrices (PWM). The ChlP data and PWM predictions showed high correlation over a wide dynamic range. This indicates high dependence between the ChlP values and the sequence hence greatly supporting the fact that TF-low affinity promoters binding is promoter sequence dependent and that the quantitative approach is advantageous. It can be seen from this that ChlP profiles can able to provide information about a wide dynamic range of specificities.