Transcription Factor motif ID

[Charlie-Big-Potato]

Hello,

I am new to this, and don't even have Seq data (yet)... I have used Galaxy to identify putative transcription factor binding sites from gene IDs using a human TFBS conserved refseq list (UCSC). The output gave me transcription factor site IDs that I can't definitively identify:

e.g. V$AHR_01 and V$AP4_Q6

I want to know if there is a list anywhere that can help me filter these IDs?

Many thanks in advance!?!?!

C-B-P

[yvan.wenger]

Hi,

Of what I see these are standard names for TF binding sites... I*just googled V$AP4_Q6 and find that http://www.broadinstitute.org/gsea/msigdb/cards/V$AP4_Q6.html

By any chance, did you compare several programs? I am trying to find a good predictor now.

Best,

Yvan

[Charlie-Big-Potato]

Hi Yvan,

Thanks for the response, sorry for my tardy reply!

Yeah - I got this site too, but wanted a more 'batch' approach since I am looking at lots of TFbinding sites in my data... I shall try to compile a list that I can share with everyone!

Best

Charlie

[simonvh]

These look like they could be TRANSFAC ID's. TRANSFAC is a commercial database: http://www.biobase-international.com...hp?id=transfac.
However, there is also a public version available http://www.gene-regulation.com/pub/databases.html. You do have to register though.

If you would like to search for de novo motifs in your data you might also want to try GimmeMotifs. It also contains a simple program to scan for known motifs in a set of sequences. Disclaimer: I wrote GimmeMotifs, so I'm very biased

[acyc]

for De Novo discovery, I would recommend Gadem program (however it works better in a seeded run, ie you know which TF you are after and have a PWM as seed).

For free programs, MotifScanner, DiRE, PASTAA (or TransFind, upgrade of PASTAA) are neat motif scanning tools.