The yellow boxes represent the average binding intensities of probes substituted at each position with other bases.
b, d, f The effects of mutations on the binding intensities of the consensus binding motif.
The average binding intensities of probes containing TGAGTCA (b), CCACGTC (d), and GGATGAC (f) were plotted.
The binding intensities of probes depend on the hybridization conditions and are reduced to various degrees.
Within the 2TF and 3TF clusters, we identified pairs of TFs whose binding was shared between two mouse species and then plotted the change in binding intensity of each TF against the other (as shown for C57BL/6J and SPRET/EiJ in Figure 4; see also Figure S4D and the section "TF Binding Intensities within Clusters Coevolve" in the Extended Experimental Procedures).
Microarrays can measure in vitro the binding intensity of a protein to thousands of probes.
In Model 2 the solution, i.e. a vector of promoter binding intensities and some other parameters, is found by best approximation of experimental data, largely on gene transcription level ratios.
Namely, the effects of PEP-promoter mutations on the intensity of Sig1-3 subindingbinding [ 9], phage type RpoTp-promoter mutations on NEP binding intensity [ 10], other studies of PEP- and NEP-dependent promoters in plastids [ 8, 11, 12] and Sig5-dependent promoter of gene psbD [ 13].
Finally, the average of the AbrB-binding signals within the individual binding sequence was calculated, as the AbrB-binding signal intensities of each binding site.
References to Figure 3, showing graphical illustrations of STAT1 binding intensities, are given for each STAT1 binding site.
