Detecting cis-regulatory binding sites for cooperatively binding proteins Export

@article{citeulike:2648023, abstract = {Several methods are available to predict cisregulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM based methods where biophysical cooperativity is not taken into account.}, author = {van Oeffelen1, Liesbeth and Cornelis, Pierre and Van Delm, Wouter and De Ridder, Fedor and De Moor, Bart and Moreau1, Yves}, citeulike-article-id = {2648023}, comment = {This article integrated prior knowledge into the discovery of cis-regulatory binding sites. Surprisingly, the results improved remarkably.}, journal = {Nucleic AcidsRes.}, keywords = {cis-regulatory, composite, discovery, motif}, number = {0}, posted-at = {2008-04-10 06:45:31}, priority = {2}, title = {Detecting cis-regulatory binding sites for cooperatively binding proteins}, volume = {0} }

TY - JOUR ID - citeulike:2648023 L3 - citeulike-article-id:2648023 N2 - Several methods are available to predict cisregulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM based methods where biophysical cooperativity is not taken into account. IS - 0 JF - Nucleic AcidsRes. TI - Detecting cis-regulatory binding sites for cooperatively binding proteins VL - 0 KW - cis-regulatory KW - composite KW - discovery KW - motif N1 - This article integrated prior knowledge into the discovery of cis-regulatory binding sites. Surprisingly, the results improved remarkably. AU - van Oeffelen1, Liesbeth AU - Cornelis, Pierre AU - Van Delm, Wouter AU - De Ridder, Fedor AU - De Moor, Bart AU - Moreau1, Yves ER -