I wonder how can I identify if the binding of a transcription factor in a chip-seq experiment to DNA is direct or indirect?
One way is to look for a motif in peaks. If your factor interacts directly with DNA than possibly a defined motif comes out. Correlates with literature search and protein structure.
For example HOMER is giving separate files for different motifs, this file contains all of the peaks but not all of them has a motif. So could it be considered as direct binding?
In example ;
(HOMER annotated motif result)
Try with different tools HOMER, MEME etc.
May be try +/- 10bp from summit of peak.
If same motif comes out than the probability increase for direct binding. Although this approach is just to get an idea that there is a direct interaction.
Thank you. Is there a way to make the probability much higher? I mean can I do something different than those approaches?
Experimental approaches can help. Bioinformatically I am not sure about more methods. Other experts can give you guidance.
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