1
$\begingroup$

I'm trying to find an easy way to get a list of putative targets of a particular transcription factor (for example, STAT1). I'm interested in targets determined using both experimental and computational evidence. I thought it should be easy to obtain such a list, but I'm having a hard time. Could anyone help me with this, preferably with specific, step-by-step instructions. As a bonus, I'm also interested in the reverse problem, which is, for a given gene, obtain a list of all transcription factors for which there is evidence that it regulates that gene.

Thanks,

Jennifer

$\endgroup$
1
$\begingroup$

If you were interested in human targets, one easy way is GeneCards, which aggregates other resources, and combines computational and (some) experimental data:

In this case the inverse problem is particularly well accessible: e.g.: scroll down to section of Genomics (e.g.: for the gene called NOTCH http://www.genecards.org/cgi-bin/carddisp.pl?gene=NOTCH1&keywords=notch1 ).

If you you were interested in obtaining all genes of a given transcription factor, you could buy a license, costing around 150 USD per year, for the GeneALaCart service of the company that runs the free genecards ( https://genealacart.genecards.org ), upload a list of all human genes (which you could for instance obtain from ncbi's ftp server), and get a spreadsheet linking transcription factors to genes.

$\endgroup$
0
$\begingroup$

You can use homer software for this, it is freeware. Homer uses a database of known motifs, and STAT1 is in there (search for STAT1 in the webpage).

With homer you can search for known motifs within the whole genome. But you can also look for all motifs within a given area of the genome. So for your bonus question, you'll need to get the genome coordinates of your gene of interest (including promoter region), and search for known motifs in that area.

You can all find it in the manual, which explains exactly which steps you need to take.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.