Sentence examples for binding sites we analyzed from inspiring English sources

To characterize sequences underlying the binding sites, we analyzed them with the p53scan algorithm [23] and found that the vast majority of the identified p53-binding sites (86% and 88% respectively) contain a p53 consensus motif irrespective of the treatment.

To identify significant peaks representing STAT binding sites, we analyzed the BED files with three independent peak-calling programs as suggested by Chen et al. [ 20]: MACS (version 1.4.2), HOMER (version 3.10) and Qeseq (version 0.2.2) with default parameters.

To determine if Erm also binds to these binding sites, we first analyzed the DNA binding domains of Erm, which contain 6 zinc fingers.

In order to understand the difference between 3' UTR and 5' UTR binding patterns for seedless sites, we analyzed the weights learned by our model for the two regions.

To determine the structural features of an extended RRE transcript including sequences beyond the primary and secondary Rev binding sites, we performed selective 2′- hydroxyl acylation analyzed by primer extension (SHAPE) analysis (Merino et al., 2005) of the 354-nt RRE RNA of HIV-1 isolate ARV-2/SF2.

To investigate if expression profile similarities were due to promoter similarities (same transcription factor binding sites (TFBS)), we analyzed the proximal promoter regions of the seven ZNF genes for (i) general properties and especially (ii) common TFBS (see Methods for details).

It is available in Additional File 7. To quantify the importance for the classification of each TF binding site motif we analyzed each one of the 1,500 CART trees produced by the method.

Because both in silico analysis and the overexpression/knock-down experiments indicated that the main effect of the c.903+469T>C mutation is to create and/or dramatically improve a binding site for SF2/ASF, we analyzed the binding of nuclear proteins to in vitro transcribed wild-type and mutant MTRR pseudoexon RNAs by a pull-down assay and Western blotting (Fig. 3).

Since the IL7Rα gene contains putative binding sites for Gfi1 [32], we analyzed IL7Rα expression levels in distinct progenitor B cells in vivo.

To determine the presence of PPARγ-RXR binding site motifs (DR1) in the PPARγ and RXR ChIP-PET genome-wide binding site data sets, we analyzed the cluster sequences using the Matinspector program, which is part of the Genomatix software suite (Genomatix, Munich).

A total of 37 CpG sites containing many overlapping transcription factor binding sites were analyzed for site-specific methylation status using bisulfite methylation sequencing analysis.