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How to find transcription factor binding for region?

I have a table with enhancer coordinate as row and number of count as the column, I want to know is there any way to find de novo TF for those regions?

 Chr   Start     End           H3k4me1    H3k27ac     ATAC_seq
1     9643292 9643794             13         16           4
1     9646837 9657496             459        922         653
1     9657582 9657828              6         12          10
1     9657962 9658273              7         29          3
chip-seq transcription_factor ensembl tf
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written by star star

2 answers

You could use BioMart. Use the Regulation -> Regulatory Evidence database. Filter by your regions and Feature type class -> transcription factor.

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written by Emily Emily

For a de novo approach, you can scan the regions for overrepresented sequences with MEME or Homer.

Alternatively, you can intersect your regions with the ReMap database to find TF binding sites based on actual ChIP-seq data.

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written by ATpoint ATpoint

Thanks for reply! is it possible to discover TF using coordinate by MEME? or it uses the sequence as INPUT?

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written by star star

Does it take more than 5 min to go to MEME website and check that information ?

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written by GouthamAtla GouthamAtla

bedtools getfasta is your friend.

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written by ATpoint ATpoint

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