Positional distribution of human transcription factor binding sites. Export

@article{citeulike:3466332, abstract = {We developed a method for estimating the positional distribution of transcription factor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs: OCT4, SOX2, NANOG, HNF1A, HNF4A, HNF6, FOXA2, USF1 and CREB1. The data were obtained from a genome-wide coverage of promoter regions from 8-kb upstream of the transcription start site (TSS) to 2-kb downstream. The number of target genes of each TF ranges from few hundred to several thousand. We found that for each of the nine TFs the estimated binding site distribution is closely approximated by a mixture of two components: a narrow peak, localized within 300-bp upstream of the TSS, and a distribution of almost uniform density within the tested region. Using Gene Ontology (GO) and Enrichment analysis, we were able to associate (for each of the TFs studied) the target genes of both types of binding with known biological processes. Most GO terms were enriched either among the proximal targets or among those with a uniform distribution of binding sites. For example, the three stemness-related TFs have several hundred target genes that belong to 'development' and 'morphogenesis' whose binding sites belong to the uniform distribution.}, author = {Koudritsky, Mark and Domany, Eytan}, citeulike-article-id = {3466332}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn752}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/21/6795}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18953043}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18953043}, day = {25}, doi = {10.1093/nar/gkn752}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {dataset, distribution, human, position}, month = {October}, posted-at = {2008-11-24 06:12:11}, priority = {2}, title = {Positional distribution of human transcription factor binding sites.}, url = {http://dx.doi.org/10.1093/nar/gkn752}, year = {2008} }

TY - JOUR ID - citeulike:3466332 L3 - citeulike-article-id:3466332 N2 - We developed a method for estimating the positional distribution of transcription factor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs: OCT4, SOX2, NANOG, HNF1A, HNF4A, HNF6, FOXA2, USF1 and CREB1. The data were obtained from a genome-wide coverage of promoter regions from 8-kb upstream of the transcription start site (TSS) to 2-kb downstream. The number of target genes of each TF ranges from few hundred to several thousand. We found that for each of the nine TFs the estimated binding site distribution is closely approximated by a mixture of two components: a narrow peak, localized within 300-bp upstream of the TSS, and a distribution of almost uniform density within the tested region. Using Gene Ontology (GO) and Enrichment analysis, we were able to associate (for each of the TFs studied) the target genes of both types of binding with known biological processes. Most GO terms were enriched either among the proximal targets or among those with a uniform distribution of binding sites. For example, the three stemness-related TFs have several hundred target genes that belong to 'development' and 'morphogenesis' whose binding sites belong to the uniform distribution. JF - Nucleic acids research SN - 1362-4962 TI - Positional distribution of human transcription factor binding sites. KW - dataset KW - distribution KW - human KW - position AU - Koudritsky, Mark AU - Domany, Eytan PY - 2008/10/25/ UR - http://dx.doi.org/10.1093/nar/gkn752 ER -