how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?

Question

[liu4gre]

I just learn to understanding ENCODE ChiP-Seq data for Transcription Factor binding. I know the narrowPeak format consists BED6+4 columns which is described in https://genome.ucsc.edu/FAQ/FAQformat.html#format12. My question is:

1. Does the region between chromStart and chromEnd mean the peak region (binding region)?
2. Does the signalValue mean the binding affinity?
3. Is it good to compare this value across cell lines to see the difference?

Answer 1

[biostart]

1) yes, it's the peak region, but it might be significantly larger than the individual TF binding site

2) This value gives the ChIP-seq peak strength. It is usually correlated with the binding affinity, but not necessarily.

3) no, the ChIP-seq enrichments in different experiments can differ for non-biological reasons