In cases where the DCC binding site overlapped with the transcriptional unit, the distance was set to zero.
The matrix was used to assign estimated binding energies, or binding scores, to each subsequence of length 22. Sequences whose highest-scoring candidate binding site overlapped with the PCR primers were discarded, leading to a set of 94 sequences which contained a candidate CAP binding site within the subsequence from the random library.
Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins).
In addition, they show that the HCDR3 binding site overlaps with the binding site of the N-terminal lobe of calmodulin (CaM), an EF enzymatic activator, consistent with a previous finding showing direct competition with CaM that results in neutralization of EF.
Basonuclin's high affinity binding site overlaps with the binding site of a dedicated and ubiquitous Pol I transcription regulator, UBF, suggesting that their binding might interfere with each other if they bind to the same promoter.
Note that at the binding site level, a prediction is considered correct when the predicted binding site overlaps with the actual binding site by at least one nucleotide.
The SRBF1 binding site overlaps with sequences required for dorsal localization of sqt RNA (i.e., Δ1 and Δ2; [ Gilligan et al., 2011], and Figure 1C,E).
In contrast, the predicted affinity of binding of TPIMS compounds to COMT was several orders of magnitude lower than to AS3MT, and the predicted binding site overlaps with the catechol binding site.
A detailed analysis of Nis (Slc5a5, Na+/I− symporter), whose transcription status is tightly regulated by Pax8 [ 7], showed a significant Pax8 binding site overlapping with the Nis upstream enhancer (Additional file 1B).
Here, a predicted peak is identified as a TP if a predicted binding site overlaps with the true starting or ending location of a spike-in DNA segment (see Figure 2).
Consistent with this, we found that the median enrichment level of Sty1 at the binding sites overlapped with the major Atf1/Pcr1 binding sites was higher than that of the Sty1 at the binding sites non-overlapped with the Atf1/Pcr1 binding sites (4-fold versus 2.3-fold higher than the array median; p-value = 3.03e-08) (Figure 6D).
