Question: Differnces between PWM derived from SELEX and ChIP-seq
gravatar for michaelchen33
5.8 years ago by
michaelchen3320 wrote:

As title.

Because SELEX experiment can detect strong binding site of TF, and ChIP-seq experiment can detect both strong and weak binding site (due to the cross-linked).

So I wonder if PWM derived from SELEX still have the strong binding site property and PWM derived from ChIP-seq still have the strong and weak binding site property.

Or,it will lose the property when these two experiments model to PWM.

Any suggestion or papers will help.


ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 5.8 years ago by michaelchen3320
gravatar for xb
5.8 years ago by
Chapel Hill, NC,USA
xb410 wrote:

The TFBSs by ChIP-seq data are usually divided into different groups (strong and weak, sometimes with an intermediate group: moderate) based on their binding strength. A common assumption is that "ChIP-seq signal values are correlated with the affinity of the TF-DNA binding" [ * ]

PWM alone helps us model the sequences at TFBSs but no such information about binding affinity, unless binding scores are also annotated.



ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by xb410

So does it means that when I transformed the experiment data like ChIP-seq to PWM, I lost the binding affinity information even through I use the strong group of ChIP-seq data?


ADD REPLYlink written 5.8 years ago by michaelchen3320

Yes, if you have the matrix only.

ADD REPLYlink written 5.8 years ago by xb410
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