CRMs are the central cis-elements that control gene expression [14]. Previously we developed a method to predict CRMs based on TF interactions [11]. This method calculates the interaction strength between two TF binding sites and then derives an empirical "potential energy" for each TF binding site. Using this method, we generated energy profiles for the promoter sequences of tissue-specific genes. An energy level less than -1 indicates the existence of a TF module. We have sensitivity of 12% and enrichment of 10 using known regulatory regions as positive control.
