Different species for different versions of TFBS

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Romain Giraud

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Mar 31, 2025, 6:14:43 AMMar 31

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Hello,

I am trying to get a complete database of murine TFBS. For that purpose I am using the pyjaspar package. I am encoutering an issue with the TFBS versions. When I use all the version, I get several versions for a TFBS, as expected. This is not ideal, since it is creating redundancy, so I then used only the latest version, as you recommend. However, when using the latest version, there are also some TFBS that are completely missing, compared with the ones I get when I retrieve all versions. I realized it is due to the fact that the specie of some TFBS is different depending on the version. I have this issue for instance with Gata1, version 1 to 3 are mouse, and 4 and 5 are human. So when my request is to get the lastest version of murine TFBS, this TFBS is not in the list. Is it safe for me to use the latest murine version then, even if it is not the latest overall ? Or are these older motifs considered not relevant anymore, and I should not use them ?

Thank you in advance.

Best regards,

Romain

Anthony Mathelier

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May 9, 2025, 2:23:25 AMMay 9

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Hi Romain.

JASPAR is species agnostic within the same taxon. If you are interesting in mouse TFBSs, you should use the latest version of *all vertebrate* profiles.