draw diagram for location of putative TF on promoter

[Wen-Jun Shen]

Dear representative:

I searched promoter region -1Kb of mouse Slc43a3 for putative transcriptional factor binding sites and find the following sites are interesting to us.  

Is there a way for the software to generate a map for the relative location of these sites on the promoter region? 

Within -1000 to 100 of mouse Slc43a3, there are many putative TF motifs. Among them:

4 PPARg, 

6 PPARg::Rxra, 

3 SREBF1

1 SREBF2,

3 STAT1

2 RUNX2

9 SP1

https://epd.epfl.ch/cgi-bin/get_doc?db=mmEpdNew&format=genome&entry=Slc43a3_1

Or any suggestions as to which software can I use to draw a diagram for this purpose?

Thank you so much!



WS

Wen-Jun Shen

Mon 1/27/2020 5:14 PM

Here is a site for downloading promoter sequence and analyze TF motifs. I am trying to see if I can export/produce a diagram with selected TF in the promoter region (still need to play with it a little more). Within -1000 to 100 of mouse Slc43a3, there

[Jairo Navarro Gonzalez]

Hello Wen-Jun,

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

If you have the coordinates for these transcription factor motifs, then you can create a custom track to display these regions around the Slc43a3_1 promoter. The following user guide can help you create a custom track using your own data, http://genome.ucsc.edu/goldenPath/help/customTrack.html#MANAGE_CT.

You may be interested in the JASPAR TFBS hub that is available on the Public Hubs page, http://genome.ucsc.edu/cgi-bin/hgHubConnect, and contains transcription factors for mouse. Using the JASPAR TFBS hub and the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), you can filter for the identifiers that you are interested in. When using the Table Browser, there is an option to filter the transcription factors by pasting the list next to the option, identifiers (names/accessions). Once the Table Browser configurations are set, you can then create a custom track by changing the output format drop-down menu to "custom track". Here is a session that uses the JASPAR TFBS 2018 hub and filtering for the motifs you shared:

http://genome.ucsc.edu/s/dschmelt/JasparTfbsCustomTrack.

You can also view our mailing list archives for further guidance. For example, these previously answered questions may be helpful for you:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/63rjALWJmKE/LNdGV9TJAAAJ
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/gIgbcTgOLzw/F8IZudwCCwAJ

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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