Using less sophisticated methods (Pearson/Spearman correlation and the method of Marstrand & Storey (2014) across fixed genomic windows), we have previously also found that correlation between time courses of TF ChIP-Seq and RNA-seq predicts functional TF target genes. This was done using public data for circadian regulators profiled at 6 time points in mouse liver.

Ref: Banks et al. Sci. Rep. 6:20649 (2016). doi:10.1038/srep20649