Sentence examples for binding sites were obtained from inspiring English sources
Constructs carrying mutant versions of miRNA binding sites (Δ96 and Δ96* binding sites) were obtained by site-directed mutagenesis.
Transcription factor binding sites were obtained from the ENCODE transcription factor ChIP track of the UCSC genome browser [ 86] (downloaded December 15 , 2011.
Tag density for RNA polymerase II binding sites were obtained by the total number of Pol II tags divided by number of promoters.
Experimentally identified transcription factor binding sites were obtained for 2,622 syntenic intergenic regions based on chromatin immunoprecipitation experiments involving 126 transcription factors (Harbison et al. 2004).
Sp1, MAZ, and PU.1 binding sites were obtained from FANTOM 4 (http://fantom.gsc.riken.jp/4/download/GenomeBrowser/hg18/TFBS_CAGE/allsites_cage_tfbs_feb09_latest.gff.gz) [ 1].
Likewise, enhancers and insulators needed to be colocalized with p300 [ 31] and cohesin [ 32, 33], respectively, the data on p300 and cohesin binding sites were obtained from the ENCODE ChIP-seq dataset [ 17].
Much more commonly a small collection of binding sites is obtained and from them a model for the TF's binding specificity is determined.
Collections of binding sites are obtained in simulation experiments where the true model for the transcription factor is known and various sampling procedures are employed.
Regardless of how the collection of binding sites is obtained, and especially important for the use of motif discovery methods, a model for the TF's specificity must be used, and usually it is some form of PWM.
While nine-fold induction of activity of full promoter-p21 reporter was achieved at concentration of 0.10 μ M of vinorelbine (P<0.01), only a 4.5-fold increase in activity of pWPdel-Bst XI reporter (only contains six Spl binding sites) was obtained under the same experimental conditions.
