Evolutionary computation for discovery of composite transcription factor binding sites Export

@article{citeulike:3420351, abstract = {Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it remained unclear whether or not composite TFBS elements, commonly found in higher organisms where two or more TFBSs form functional complexes, could also be identified by using this approach. Here, we present an important refinement of our previous algorithm and test the identification of composite elements using NFAT/AP-1 as an example. We demonstrate that by using appropriate existing parameters such as window size, novel-scoring methods such as central bonusing and methods of self-adaptation to automatically adjust the variation operators during the evolutionary search, TFBSs of different sizes and complexity can be identified as top solutions. Some of these solutions have known experimental relationships with NFAT/AP-1. We also indicate that even after properly tuning the model parameters, the choice of the appropriate window size has a significant effect on algorithm performance. We believe that this improved algorithm will greatly augment TFBS discovery. 10.1093/nar/gkn738}, author = {Fogel, Gary B. and Porto, V. William and Varga, Gabor and Dow, Ernst R. and Craven, Andrew M. and Powers, David M. and Harlow, Harry B. and Su, Eric W. and Onyia, Jude E. and Su, Chen}, booktitle = {Nucl. Acids Res.}, citeulike-article-id = {3420351}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn738}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/21/e142?etoc}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18927103}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18927103}, day = {1}, doi = {10.1093/nar/gkn738}, journal = {Nucl. Acids Res.}, keywords = {algorithm, genetic}, month = {December}, number = {21}, pages = {e142+}, posted-at = {2009-07-21 04:40:07}, priority = {2}, title = {Evolutionary computation for discovery of composite transcription factor binding sites}, url = {http://dx.doi.org/10.1093/nar/gkn738}, volume = {36}, year = {2008} }

TY - JOUR ID - citeulike:3420351 L3 - citeulike-article-id:3420351 N2 - Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it remained unclear whether or not composite TFBS elements, commonly found in higher organisms where two or more TFBSs form functional complexes, could also be identified by using this approach. Here, we present an important refinement of our previous algorithm and test the identification of composite elements using NFAT/AP-1 as an example. We demonstrate that by using appropriate existing parameters such as window size, novel-scoring methods such as central bonusing and methods of self-adaptation to automatically adjust the variation operators during the evolutionary search, TFBSs of different sizes and complexity can be identified as top solutions. Some of these solutions have known experimental relationships with NFAT/AP-1. We also indicate that even after properly tuning the model parameters, the choice of the appropriate window size has a significant effect on algorithm performance. We believe that this improved algorithm will greatly augment TFBS discovery. 10.1093/nar/gkn738 IS - 21 JF - Nucl. Acids Res. TI - Evolutionary computation for discovery of composite transcription factor binding sites VL - 36 T2 - Nucl. Acids Res. SP - e142 KW - algorithm KW - genetic AU - Fogel, Gary AU - Porto, William AU - Varga, Gabor AU - Dow, Ernst AU - Craven, Andrew AU - Powers, David AU - Harlow, Harry AU - Su, Eric AU - Onyia, Jude AU - Su, Chen PY - 2008/12/01/ UR - http://dx.doi.org/10.1093/nar/gkn738 ER -