How to find transcription factor binding for region?

Question

[star]

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

Answer 1

[Emily]

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

Answer 2

[ATpoint]

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.

[star]

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

[ATpoint]

bedtools getfasta is your friend.

[GouthamAtla]

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