Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data Export

@article{citeulike:3145652, abstract = {Molecular interactions between protein complexes and DNA mediate essential gene-regulatory functions. Uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) has recently become the focus of intense interest. We here introduce quantitative enrichment of sequence tags (QuEST), a powerful statistical framework based on the kernel density estimation approach, which uses ChIP-Seq data to determine positions where protein complexes contact DNA. Using QuEST, we discovered several thousand binding sites for the human transcription factors SRF, GABP and NRSF at an average resolution of about 20 base pairs. MEME motif-discovery tool–based analyses of the QuEST-identified sequences revealed DNA binding by cofactors of SRF, providing evidence that cofactor binding specificity can be obtained from ChIP-Seq data. By combining QuEST analyses with Gene Ontology (GO) annotations and expression data, we illustrate how general functions of transcription factors can be inferred.}, address = {[1] Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305, USA. [2] These authors contributed equally to this work.}, author = {Valouev, Anton and Johnson, David S. and Sundquist, Andreas and Medina, Catherine and Anton, Elizabeth and Batzoglou, Serafim and Myers, Richard M. and Sidow, Arend}, citeulike-article-id = {3145652}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth.1246}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nmeth.1246}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18711362}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18711362}, day = {17}, doi = {10.1038/nmeth.1246}, issn = {1548-7091}, journal = {Nature Methods}, keywords = {chip, genome, large, scale}, month = {August}, number = {9}, pages = {829--834}, posted-at = {2009-04-23 00:31:43}, priority = {2}, publisher = {Nature Publishing Group}, title = {Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data}, url = {http://dx.doi.org/10.1038/nmeth.1246}, volume = {5}, year = {2008} }

TY - JOUR ID - citeulike:3145652 L3 - citeulike-article-id:3145652 N2 - Molecular interactions between protein complexes and DNA mediate essential gene-regulatory functions. Uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) has recently become the focus of intense interest. We here introduce quantitative enrichment of sequence tags (QuEST), a powerful statistical framework based on the kernel density estimation approach, which uses ChIP-Seq data to determine positions where protein complexes contact DNA. Using QuEST, we discovered several thousand binding sites for the human transcription factors SRF, GABP and NRSF at an average resolution of about 20 base pairs. MEME motif-discovery tool–based analyses of the QuEST-identified sequences revealed DNA binding by cofactors of SRF, providing evidence that cofactor binding specificity can be obtained from ChIP-Seq data. By combining QuEST analyses with Gene Ontology (GO) annotations and expression data, we illustrate how general functions of transcription factors can be inferred. IS - 9 JF - Nature Methods SN - 1548-7091 AD - [1] Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305, USA. [2] These authors contributed equally to this work. EP - 834 TI - Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data PB - Nature Publishing Group VL - 5 SP - 829 KW - chip KW - genome KW - large KW - scale AU - Valouev, Anton AU - Johnson, David AU - Sundquist, Andreas AU - Medina, Catherine AU - Anton, Elizabeth AU - Batzoglou, Serafim AU - Myers, Richard AU - Sidow, Arend PY - 2008/08/17/ UR - http://dx.doi.org/10.1038/nmeth.1246 ER -