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  • Transcription Factor motif ID

    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

  • #2
    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

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    • #3
      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

      Comment


      • #4
        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

        Comment


        • #5
          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.

          Comment

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