How to use JASPAR to find TF binding site?

Sanjukta Ghosh

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Oct 31, 2020, 10:15:53 AM10/31/20

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Hello all, I just got introduced to JASPAR in a paper, PMID: 31091119.
I wish to use it to figure out TF binding sites on some genes.
Can somebody please give an outline as to how to use this site to find TF binding sites?

Thanks. :)

Oriol Fornés

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Oct 31, 2020, 2:16:57 PM10/31/20

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Dear Sanjukta,

If you were interested in human (or another model organism), I recommend that you use the JASPAR genome tracks at the UCSC genome browser:

http://jaspar.genereg.net/genome-tracks/

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Oriol Fornés Crespo, PhD
Deputy Group Leader / Wasserman Lab
or...@cmmt.ubc.ca

Centre for Molecular Medicine and Therapeutics (CMMT)
Dpt. of Medical Genetics / University of British Columbia
BC Children's Hospital Research Institute
950 W 28th Ave, Room 3109, Vancouver, BC V5Z 4H4, Canada

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Sanjukta Ghosh

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Oct 31, 2020, 2:23:37 PM10/31/20

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Okay. Thanks. :)

Anthony Mathelier

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Oct 31, 2020, 2:58:33 PM10/31/20

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You could also use the TFBSs from UniBind (https://unibind.uio.no/) that are predicted using JASPAR PWMs in ChIPseq peaks.

Best

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Sanjukta Ghosh

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Nov 2, 2020, 11:48:15 AM11/2/20

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Thanks, Anthony but my model of study is mouse. Is there anything you can recommend regarding it?

Anthony Mathelier

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Nov 2, 2020, 2:04:28 PM11/2/20

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Dear Sanjukta,

We have recently been expanding UniBind to 9 species, including mouse. The new data will be soon (in the next few weeks) provided on the UniBind website along with the corresponding manuscript on bioRxiv. For now, you can find it at https://testunibind.uio.no/ temporarily.

I hope it helps.

Best
AM

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Anthony

Sanjukta Ghosh

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Nov 3, 2020, 9:33:23 AM11/3/20

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Thank you so much!!

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