Sentence examples for binding site we checked from inspiring English sources
For each lifted mouse binding site we checked if >10% of the site was overlapped by a human site, or vice versa.
For the 44 (109-65) interactions not reported in RegulonDB for which we found a phylogenetically conserved binding site, we checked for functional relationships between the regulator and the target.
In order to check whether S' is a potential binding site, we compare its profile score with the user-specified threshold, λ ∈ [0,1].
In order to determine the potential mechanisms for the gain/loss of miRNA binding sites, we further investigated and checked the alignments of binding regions in the 17 WGD gene pairs.
To identify DNA sequence motifs of OmpR binding sites, we first used the MEME software tool28 with the genomic sequences of binding sites.
If we thus identified a DNA sequence that resembled known binding sites of PdhR, we checked whether the corresponding region coincides with a part of the promoter known to be phylogenetically conserved upstream of genes in ten proteobacterial genomes [ 35, 36].
When the asymmetric unit was found to differ from the biological unit, the ligand binding site was carefully checked.
For the binding sites lost in human, we checked if a human-specific binding site is located +/-10 kb (max 10 kb between the midpoints of the two binding sites) from the original lifted binding site.
Prediction of transcription factor binding sites and their conservation is performed in two steps: first we scan the human DNA sequence for binding sites and next we check whether the predicted sites belong to a sequence fragment conserved with respect to the DNA sequence of another organism.
Next, the predicted human binding sites are checked whether they belong to a sequence fragment conserved in another species close to the orthologue of a studied gene.
