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Some of our AR binding sites that we found to be localized in intergenic regions may be localized to these TARs.
All three OBF-1 binding sites that we identified are located in a region upstream of the λ5 gene that has been recently described as a locus control region.
Four sets were designed to amplify promoter regions containing Stat3 putative binding sites that we previously studied in MM1 cells (Fig. 3), and an additional set (primer set 5) was designed to amplify a region lacking GAS-like elements.
We concentrated on those binding sites that we could see from our fibril model were located at the fibril surface in the mature stable form of the collagen fibril, in each D-period at ∼0.74D and ∼0.87D within the e1 and d microscopy bands respectively, the d band sequence being: 899-GKNGDRGEPGP-909.
Based on the significant binding sites that we obtained from our FDR approach, we first counted the number of crosslink events within each binding site for each sample type.
It was only after extending our definition of 'deleterious' to include 5′-UTR variants that lie in regions annotated by the ENCODE consortium (22) as transcription factor binding sites, that we uncovered the c.-540G>A variant.
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We selected binding sites that passed the P < 0.005 cutoff and did not apply any filter based on evolutionary conservation.
To identify the motifs utilized for TR4 recruitment at the 346 TR4 binding sites that are also occupied by ELK4, we performed motif analysis using MEME.
These observations were further strengthened when we examined CTCF binding sites that were "partially" conserved.
We identified 44,887 putative binding sites that belong to 39,384 pairs of miRNA and lincRNA.
We searched for transcription factor binding sites that were common to these 28 genes.
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