How to choose a transcription factor binding motif

[jennaho...@gmail.com]

Dear, 

I have a question regarding the different transcription factor binding sites variants. For example, if I search for NF-kB, I get 4 different NF-kB1 variants. How should I choose which variant to use for my promoter analysis? On which factors does this depend?

Another question; can I use the same transcription factor binding sites for human for different animal species (such as macaque, mouse and rat)?

Thank you in advance, 

Best, 

Jenna 

[Anthony Mathelier]

Dear Jenna,

Thanks for your interest in JASPAR. The 4 different profiles available for NFKB1 correspond to different versions. You should use the latest version (MA0105.4 in this case). Indeed, it means that the curators found this profile of better quality compared to the previous one.

JASPAR provides TF binding profiles per taxa, which could be used for any species in the same taxa.

Best
AM

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