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The binding sites of most TFs are short (5 20 bp) [44] degenerate sequences that occur frequently in the genome by chance [41], which causes many sequences with similarity to known TFBSs that are not functional to occur in the genome [41].
The binding sites of most TFs show significantly higher structural conservation in more than one specific positions.
It might be a while before binding sites of most TFs are mapped in a majority of tissues and cell lines.
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The binding site of most active herbal components was site 1 in subdomain IIA of HSA.
The ATP-binding sites of most protein kinases share similar features.
In the contrary, despite that some down-regulated genes were found to harbor putative CRE sites (Addition file 3), no such a conserved motif can be retrieved from the promoter sequences of these genes, thus indicating that the CcpA-binding sites of most of the down-regulated genes are atypical or they might be indirectly regulated by CcpA.
A previous global analysis of DNA binding sites for most of the transcription factors of yeast provided the first evidence to suggest that Yap1p may regulate the expression of transcription factors [ 30].
Consistent with the predictions of the RISC-competition model, we found that ~60% of the mRNAs enriched for binding sites of those miRNAs most highly expressed in pre-transfected HEY cells were significantly over-represented among mRNAs up-regulated after miR-128 transfection.
Conclusions that are most consistent with the binding data indicated a single binding site on most proteins, irrespective of the probe or the protein, with only one exception noted so far.
This result suggests that PWMs may be sufficient to model binding sites for most of the transcription factors in this study, whereas perhaps other transcription factors may require more complex binding site models.
However, the number of binding sites for most transcription factors modelled in TRANSFAC is fairly low and this limits the conclusions that can be drawn from this analysis.
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