However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB).
Because approximately 89% of these genes were bound by σ, we measured the intensity of σ binding in Δ rpoS during stationary phase with ChIP-chip experiments, and compared the binding intensity between up-regulated and down-regulated genes.
The cetylpyridinium chloride (CPC -precipitation assay has been used for investigating binding affinity [ 29] and the assay in our study demonstrated that USP17 subfamily proteins interaCPC -precipitation bassayon thascomparison of beening intensity between endogenousednd exogenous hyaluronans (for. 7A, lanes 4 and 5).
This assumption is valid when the binding regions represented by the common peaks show a much higher level of colocalization between samples than that expected at random, and thus binding at the common peaks should be determined by similar mechanisms and exhibit similar global binding intensity between samples.
Thus, in clusters of combinatorial TF binding, differences in binding intensities between species appear to occur coordinately, and the component HNF4A, CEBPA, and FOXA1 binding sites increase and decrease their genomic binding strengths in a coherent, directional manner.
Although several recent studies have used NGS with DamID (Carl and Russell, 2015; Clough et al., 2014; Lie-A-Ling et al., 2014; Wu and Yao, 2013), these have relied upon a comparison of peak binding intensities between read-count-normalized Dam-fusion and Dam samples.
The variation in maximal pimonidazole-binding intensity between tumours and within ROIs is another indication for the existence of 'oxygen conformer cell'.
Remarkably, we found a strong association between the JIL-1 binding intensity and the maintenance of clusters including OBP genes (Spearman's rank correlation coefficient: ρ = 0.617, P = 0.010; fig. 4 D).
However, striking differences in the binding intensity exist between Oct4+/+ and Oct4+/− ESCs.
We quantitated the binding intensity of the top 10% of the binding sites for all three ChIP-Seq experiments and performed comparisons between wild-type and Clock Δ19 /Clock Δ19 animals.
