Hi researchers,
I'm searching the answer at the same time when I put the question. Appreciate any experience for this question.
1.For a know transcription factor (TF), how to check its binding motif? Is there a database that you input a TF name and it will show all the predicted or validated binding sites of this TF?
2.And for a certain gene, how to check which TF can activate or inhibit its transcription?
If the result is prediction, how to check the reliability? Is there a p value or something?
Thanks！
The best way to go about the question is to mine chip seq dataset on your TF of interest (ideally in your cell line of interest). Since that is most frequently not available, an alternative approach is to look for evolutionary conserved regions in noncoding regions. Alternatively, you can address defined regions experimentally by tiling gRNAs throughout the region and identify functionally important regions.
1. UniPROBE by Marth Bulyk lab, or try JASPAR. If not known, you can derive it from ChIP-Seq using tools such as MEME-ChIP.
2. Get PWM of the TF of your interest, and overlay it onto the genome using tool such as FIMO.
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