Hi Sadra maybe you can find useful the following info:

1) In the available info of ENCODE you can find per TF, the list of genes that are found as targets by ChIP-Seq https://maayanlab.cloud/Harmonizome/dataset/ENCODE+Transcription+Factor+Targets.

2) Another possibility if you have i) a list of TFs binding motifs (or you find the frequencies matrixes and logos for your TFs of interest over a database like JASPAR: https://jaspar.genereg.net or MEME https://meme-suite.org/meme/) and ii) the sequences of your genes of interest you can try to see if there is any probability of finding a match considering the frequencies matrix and defining the binding patterns.

3) In a visual way, inside USCS browser you can visualize the ENCODE CHip-Seq data and the JASPAR database too but not for all genome assemblies.

Kind regards,

Mar

One nice way to start is to determine which TF are enriched in the promoters of the set of genes coding for your transcripts from RNA-seq. This can be done by oPOSSUM3 Article oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Repres...

Also, here an example of a recent paper from our group that uses this method to identify TF involved in norepinephrine responses Article Effects of long-term norepinephrine treatment on normal immo...

Good luck!

alvaro

Thank you so much for your good recomendations.