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ajsn6c 07-21-2016 01:57 PM

ChIP-seq and Peak calling
I have a simple question that I would like some opinions on. If a transcription factor is highly expressed (protein) in one cell and say now that the expression of is halved because of knock down experiment and you do ChIP-seq on both conditions, would you expect a similar amount peaks found using MACS, or rather a lower level of signal intensity in the knock down condition. I would think just a lower signal, but I'm curious what you all think


dpryan 07-22-2016 12:32 AM

My guess is that some peaks would be largely unaffected while others would vanish completely. This is mostly because I would guess that in some regions the factor would be more heavily recruited and/or bind with higher affinity, thereby sponging up the available supply. Of course, one could also envisage a scenario wherein signal intensity is roughly halved globally (of course, scaling might screw this up), or decreased even further (e.g., if binding can only occur as dimers and the probability of dimerization is now lower).

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