You use ChlP-seq to identify the binding sites of your favorite transcription fa

Question

You use ChlP-seq to identify the binding sites of your favorite transcription factor, p53. A colleague who is studying colon cancer walks into your office incredulous that your list fails to find a p53 binding site in front of his favorite gene, gut1. You promise to double check your analysis of your ChIP and find that directly over the promoter of gut1 there is a small region with 25 reads in your ChlP-seq IP sample. What happened? Your peak caller must have something wrong with it because it didn't find this region O This region is clearly not bound by p53 O You should check the background (whole cell extract) sample first in this region before making any conclusions O Just change the parameters to your peak caller until it finds this peak

Explanation / Answer

this region is clearly not bounded by p53 so list fails to find a p53 binding site in front of his favorite gene

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