Way to Download a List of TF Motifs

[Joy Santos]

Hello! 

I was wondering if there was a way to download a full list of the transcription factor binding motifs used to generate the PWMs and PFMs in the database?

Thanks! 

[loka...@gmail.com]

Hi Joy

We are not sure of understanding your question.

Do you mean the TF binding sites (DNA sequences) used to built the PFMs?

This is possible although not for all motifs, for those motifs that were generated in house (that the JASPAR team generated using a motif discovery pipeline on ChIP-seq/-exo datasets) we do have the sites provided as BED/FASTA files.

Here is an example: http://jaspar.genereg.net/matrix/MA0482.2/

You can download the TF binding sites on the 'Binding sites information' section, below the 'Profile summary' (We discover a bug regarding the matrix sites, we are working on it and it will be fixed in the upcoming JASPAR release, publicly available in ~1 month)


However, a large proportion of the motifs available in JASPAR come from external sources, for example from SELEX or PBM experiments, in such cases, we do not have the sequences used to build the PFMs.


I hope this information is helpful

Best regards,

Jaime

[Susana Posada]

Dear Jaime,

I am wondering how difficult/feasible would be to collect comparable information to the 'Binding sites information' for the motifs that come from external sources. Could you also comment about what are the external sources?

thank you very much!

Very best,

Susana

[loka...@gmail.com]

Hi Susana

In the documentation section (https://jaspar.genereg.net/docs/) we describe the difference in internally/externally generated motifs.

All the internally generated motifs (at least since the 2018 release that is when I started to work in JASPAR) come from in vivo methods (ChIP-seq/-exo), and in these cases we can detect the genomic positions used to build the matrices.

However,  the externally generated are motifs that other research groups published, and for in vitro derived motifs (for example those coming from SELEX or PBM) it is impossible to obtain the binding sites  (unless the authors provide them) 
In the 2022 release this is the list of resources where we took the motifs before the curation:

- Human TF dimers , CAP-SELEX, and NCAP-SELEX from Jussi Taipale's group - Human zinc finger motifs inferred with the RCADE method from Nahafabadi's group - Ascidian TF motifs derived from SELEX-seq (Aniseed)
- Cis-bp plant motifs derived from protein-binding microarrays
For the previous JASPAR releases, you can check this list in the supplementary material of their manuscript

Let me know if this is clear

Best regards

Jaime