Which experiments generate Position Frequency Matrix?
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6 weeks ago
arriyaz.nstu ▴ 30

From the JASPAR database, I can download Position Frequency Matrix (PFM) for transcription factors. My question is, how can we get such PFM for a transcription factor? Is there any experimental method or technique like ChIP-seq to generate PFM?

Position-Frequency-Matrix • 445 views
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5 weeks ago
ATpoint 82k

Yes, ChIP-seq or similar methods that assay the DNA binding of a protein. But for a reliable matrix you don't need one or two but many datasets. That is why curated repositories such as JASPAR or (my favorit) HOCOMOCO are valuable, as they base their PFMs on many datasets for the same protein.

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That was very helpful. Thank you for your reply.

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