HOMER peak-motif relationship as direct-indirect binding

Question

[buffealo]

Hello,

I am conducting ChIP-seq analysis. I have HOMER annotated motif list assigned to every peak in MACS2 result. I have an example

(by the way I could not fit all of the information that excel files has but in the first column there are simply peak names)

I wonder, could it be interpreted as; if there is motif(like in the first line) of the subjected TF factor is directly binding, and if there is no motif found(like in the second line) there is indirect binding.

Thank you for any idea in advance!

[seidel]

You need to add more information about what you're trying to accomplish. Your ChIP Seq experiment for a given factor highlighted certain segments of the genome. Any given segment of the genome may contain a variety of motifs. If you search randomly chosen segments of DNA for HOMER motifs you will find them - this means nothing on its own. One the other hand, one expectation you can have, is that highly scoring peaks in your ChIP Seq experiment should be enriched for motifs for the factor you used in the experiment. What is your experiment? What question are you trying to answer?

[buffealo]

I am trying to distinguish direct and indirect binding. I am working with breast cancer cell line and my transcription factor (also the antibody of the experiment) is ERalpha. So that HOMER gives ERE motif(my TF binds) as first ranked motif in my samples. Since ER alpha can bind as complex or individually to the genome, I am trying to classify the known1.motif (which contains only ERE information) results as direct-indirect binding. As I added above, some peaks have results and some oh them do not. I thought that it could be an idea to separate them according to that. I hope I could explain myself clearly. I am looking for your response. Thank you.