I would like to perform correlation analysis between gene expression and TF binding in control and KD condition. So what I have till now is gene expression in control and KD condition and normalized tag count of different transcription factor obtained from Homer annotatePeaks.pl for merged peaks of all the TF. One approach I am thinking to take average tag count for all the genes and correlated with expression or another way correlate fold change of TF binding with fold change in expression. Do you think its a right way to do this analysis ? If not, please suggest some approach or any tools that perform this type of analysis. Any comments or suggestions will be highly appreciated.