question Re: JASPAR transcription factors search

[Tali Lanton]

Dear UCSC customer service,

I am interested in  learning about the binding sites of transcription factors in the promoter region of genes. I am able to view extensive lists of transcription factors using the JASPAR track on the UCSC website, however I can not seem to figure out how to download the lists (such as the list of transcription factors viewed in the snapshot below ).

Is there a way to download a list of transcription factors and binding sites from a region of interest , so that I can view it in microsoft excel?

Thanks for your help,

Tali 

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Tali Lanton, PhD
Goldyne Savad Institute of Gene Therapy
Hadassah University Hospital
POB 12000
Jerusalem 91120 Israel
Tel 972-2-677-8883
FAX 972-2-643-0982
Mobile phone: 052-898-5950

[Jairo Navarro Gonzalez]

Hello Tali,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can use the Table Browser to download a region of interest in a tab-separated file. With the JASPAR TFBS hub connected, go over to the Table Browser tool, http://genome.ucsc.edu/cgi-bin/hgTables. You can then choose the JASPAR TFBS hub from the "group" drop-down menu, then select the track you want to use for your analysis. For my example, I will be using the "JASPAR2020 TFBS hg38" track.

Once your track is selected, you can then define the position of interest, or positions using the "define regions" button. With the region of interest defined, you can then change the output format and then enter an output filename to download the output as a file. After you have entered a name for the file, click "get output" to download the data.

If you are new to using the UCSC Genome Browser, you may be interested in reviewing our online training page or the mailing list archives:

http://genome.ucsc.edu/training/
https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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