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Microarrays can measure in vitro the binding intensity of a protein to thousands of probes.
Recent technologies measure the binding intensity of a TF to many DNA sequences [e.g. protein-binding microarray (PBM) (Berger et al., 2006) and MITOMI [ Fordyce et al., 2010)].
Coevolution in this case means that, if the TF binding intensity of a component TF within a cluster differs between two mouse species, then the intensities of cobound TFs are more likely to differ as well and in a coherent direction.
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We background-corrected probe expression levels for non-specific binding based the distribution of binding intensities of a set of "anti-genomic" probes of a similar GC content to the probe of interest.
PrP-overexpressing T-cells [18] from blood were stained in two steps using purified POMs or 6H4 in equal concentrations and fluorescently labeled anti-mouse IgG, in order to compare binding intensities of all mAb as previously described [4].
Next we compared the expression levels of genes in adipocytes to the binding intensity of TAF7L and found a strong positive correlation in the three expression groups.
DOI: http://dx.doi.org/10.7554/eLife.00426.017 Heat map analysis of the 1916 sites that are co-occupied by both USF1 and CLOCK BMAL1 in Clock Δ19 /Clock Δ19 mutant animals reveals a dramatic increase in binding intensity of USF1 in mutant mice.
In particular, the results showed a significant increase in binding intensity of ERα in E2-treated condition when compared to that in the control condition (i.e. ~400 in E2-treated condition verse ~50 in the control condition for chr20 52000001 53000000; Table 2).
These technologies synthesize a large set of DNA sequences and measure the binding intensity of the TF to each of those sequences.
Ciolkowski et al. [ 58] reported that Arabidopsis AtWRKY6 and AtWRKY11 bind well to W-boxes that have a G residue directly 5' adjacent to the element, whereas AtWRKY26, AtWRKY38, and AtWRKY43 bind to the same motif if the 5'-residue is a T, C, or A. Furthermore, bacterial challenge changed the binding intensity of proteins to W-boxes [ 9].
The binding intensity of biotinylated anti-CD20 to B cells detected with CD19+ was analyzed by FACSCalibur.
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