Sentence examples for binding sites we set from inspiring English sources

Since the median coverage of an NRSE is 21 bp while the stripe CRMs are known to be densely populated with binding sites, we set m = 5 for the stripe WPHs and m = 3 for the NRSF WPHs.

To get significantly associated co-TFs with a given set of STAT binding sites, we set the normalized motif-covered site threshold as 0.2 and the motif enrichment score threshold as 1.5.

Hybridizations were performed as previously described by Follows et al. In order to locate potential Hox-TALE functional binding sites, we set out to identify cis-regulatory modules based on their sensitivity to nuclease digestion and a corresponding location of consensus-binding-site sequences.

For the detection of the conformational changes and the localization of the quinone binding site, we set up a combination of site-directed spin labeling and EPR spectroscopy.

Based on the number and spatial distribution of these binding sites, we calculate a set of probabilistic features that are used to make predictions for novel ceRNAs of PTEN.

To analyze the specificity of presence of AP-1 and SP1 binding sites, we generated a set of 100 random 1 kb sequences, which were analyzed in the same way, as our primary dataset.

To investigate the association between gene expression activity and the occupancy of CTCF binding sites, we used a set of histone modification data from the Broad Institute [ 22] available from the ENCODE project (Additional file 6: Table S2), in combination with counts of histone marks in the flanking regions of each CTCF binding site (Fig. 2, Fig.  3a).

Based on the global chip array results with potential SALL4 binding sites, we designed 3 sets of primers for the ABCA3 promoter region (one was from a peak region, two sets were designed on non-peak regions for negative controls) and two sets of primers for the ABCG2 promoter regions (Figure 4A).

While we expected that over-expression of an FFRP would reveal the most comprehensive set of binding sites, we also expected that only a subset of these binding sites would be conditionally functional in any given environment.

To analyze each promoter set for common TF binding sites, we used the MatInspector software [ 28].

To compare the selected sets of the putative binding sites, we computationally predicted all binding sites in the human genome using our affinity data (Additional file 5).