Up and down stream TFs

Question

[malleshsjgc]

Hello, I was isolated a gene from Wheat and heterologously expressed for functional validation How to find the up stream and down stream TFs for this single gene? I am grateful if any one suggest a software and process to find TFs

Thanking yu, MM

[Chirag Parsania]

You mean to say upstream sequences of a gene ?

Answer 1

[Alex Reynolds]

You could use FIMO in the MEME suite to find TF binding sites for your genome of interest.

You'll need to provide models; for wheat, maybe wDBFT could help, or PlantRegMap. Or you could try using the MEME tool itself to do discovery (to generate models) and then run FIMO on those models to get binding sites.

Once you have binding sites, you could use a tool like BEDOPS closest-features to locate the nearest TF binding sites up- and downstream of your gene(s) of interest:

$ closest-features genes.bed bindingSites.bed > answer.bed