Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Export

@article{citeulike:2927430, abstract = {With the increasing number of eukaryotic genomes available, high-throughput automated tools for identification of regulatory DNA sequences are becoming increasingly feasible. Several computational approaches for the prediction of regulatory elements were recently developed. Here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc.columbia.edu/Target\_Explorer/}, address = {Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, USA.}, author = {Sosinsky, A. and Bonin, C. P. and Mann, R. S. and Honig, B.}, citeulike-article-id = {2927430}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkg544}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/31/13/3589}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12824372}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12824372}, day = {1}, doi = {10.1093/nar/gkg544}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {columbia, regulatory\_elements}, month = {July}, number = {13}, pages = {3589--3592}, posted-at = {2008-07-13 18:58:52}, priority = {2}, title = {Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors.}, url = {http://dx.doi.org/10.1093/nar/gkg544}, volume = {31}, year = {2003} }

TY - JOUR ID - citeulike:2927430 L3 - citeulike-article-id:2927430 N2 - With the increasing number of eukaryotic genomes available, high-throughput automated tools for identification of regulatory DNA sequences are becoming increasingly feasible. Several computational approaches for the prediction of regulatory elements were recently developed. Here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc.columbia.edu/Target_Explorer/ IS - 13 JF - Nucleic acids research SN - 1362-4962 AD - Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, USA. EP - 3592 TI - Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. VL - 31 SP - 3589 KW - columbia KW - regulatory_elements AU - Sosinsky, A AU - Bonin, CP AU - Mann, RS AU - Honig, B PY - 2003/07/01/ UR - http://dx.doi.org/10.1093/nar/gkg544 ER -