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The authors introduce "binding intensity" in the paragraph and use it throughout the introduction without proper explanation.
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Increased binding intensities in the 4M KOH PC extracts of MYB4-OX lines were for mAbs that recognize pectic arabinogalactan (RG-I/AG) epitopes (Additional file 1: Figure S6, white boxes and Figure 5a).
The intensity of 0.5 in psbA is weighted with a reducing coefficient to reflect a lower quality of ycf1-33/34 and ndhF-320 promoters with respect to psbA-77, as follows from the experimental data on the effect of promotersromoter mutations on the binding intensity in chloroplasts of mustard [ 9].
In response to this concern, Tables 2 and 3 now contain standard deviations of transcription level ratios obtained in Model 1 using binding intensities given in the legends and estimated in Model 2. Loci 1 and 2 are found to behave very similarly in the model and experiment (changes in transcription levels are similar, refer to Table 2).
The knockout was modeled for Sig3 and Sig4 under the same values of the polymerase-promoter binding intensities as in the wild type.
This attests that RNA polymerase binding intensities predicted in the model correspond well to measured gene transcription level changes.
Log2 fold changes in binding intensity between the three epithelial subsets were computed for each miRNA using edgeR's glmFit function, setting the negative binomial dispersion to 0.05 and the prior count to 1 [ 36].
The crystal binding intensity contributing from all the atoms in the solid to the Au-E4f electrons in the bulk is determined to be −2.87 eV.
It is possible that for certain active promoters, RPol II binding intensity changes but the signal in both conditions are higher comparing to the background (active in both conditions).
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).
The observation of a same binding intensity for IN, pep-a4, K159 and HTH already suggests that the epitope coincides with pepa4 and is freely accessible to the antibody in the enzyme.
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