Add a new TF

[Rafael Soler Ortuño]

Hello,

How could a new transcription factor be included in the JASPAR database? What would the application process be?

All the best,

Rafa

[loka...@gmail.com]

Hi Rafa

All motifs in the JASPAR CORE collection have two references in the literature, the first is where the motif comes from and  a second one supporting the motif (ideally in the supporting reference  the motif was found with a different technique or in a different setting (cell-type, tissue, growing condition, etc))


Example: 

https://jaspar.genereg.net/matrix/MA0112.3/   (see the table at the left side)

The source of the motif for ESR1 is this publication (https://pubmed.ncbi.nlm.nih.gov/23332764/) where the motifs were detected with SELEX-seq. The supporting reference (validation)  is a paper where a similar ESR1 motif was discovered in a ChIP-seq experiment (https://pubmed.ncbi.nlm.nih.gov/19339991/)


So, we need  1) the motif, 2) Source reference , and 3) Validation reference


In case you only have the source reference and the motif, you can send it to anthony.mathelier AT ncmm.uio.no and our team of curators will search for the validation reference and evaluate the motif quality.
In case we don;t find it, we could add it to the Unvalidated collection.


Also, it could be the case that your motif is already in the Unvalidated collection: https://jaspar.genereg.net/collection/unvalidated/  if this is the case, you can upload the required information in the dedicated section (community curation, on top) at each motif in this collection
Example: https://jaspar.genereg.net/matrix/UN0158.1/   

I hope this info help

Best regards

Jaime

[Rafael Soler Ortuño]

Thank you so much Jaime! :)

El dia dijous, 16 de desembre de 2021 a les 11:33:52 UTC+1, loka...@gmail.com va escriure: