Inquiry Regarding Transcription Factor Binding Site Identification in EPD

[Shah, Mohd (NIH/NEI) [F]]

Hello,

I hope this email finds you well. My name is Dr. Mohd Hussain Shah, and I am currently working at NIH-USA. I have retrieved the promoter sequence of a gene using the EPD tool and was wondering if it is possible to use the same tool to identify transcription factor binding sites.

If so, could you kindly assist me with the steps to perform this analysis?

Thank you for your time and assistance.

Sincerely,
Dr. Mohd Hussain Shah

 

[CCG EPFL]

You can use the "Search Motif Tool" on the promoter entry viewer page, for instance go to:

https://epd.expasy.org/cgi-bin/epd/get_doc?db=hgEpdNew&format=genome&entry=EMC8_1

Then fill out the Search Motif Tool menu near the bottom of the page as follows:

Note the Selections "Transcription Factor Motifs" and "SP1". According to the image, this promoter contains several SP1 binding sites 500-1000 bp upstream of transcription initiations site.

Philipp