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Differnces between PWM derived from SELEX and ChIP-seq

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.

Thanks

chip-seq tfbs selex position weight matrix
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updated by Ram Ram • written by michaelchen33 • michaelchen33

1 answer

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.

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updated by Ram Ram • written by xb xb

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?

Thanks

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updated by Ram Ram • written by michaelchen33 • michaelchen33

Yes, if you have the matrix only.

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written by xb xb

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